Most meta-relevant legendaries now and going forward

You are pretty much spot on. For the 4 'best legendaries' you mentioned:

Rayquaza- pretty much a no-brainer. It shares the highest Base stat total in the games with mewtwo (mega). Has at least a month of use for Latis and still super useful for the gen 4 dragon legendaries further away.

AND when it gets outdone as a dragon, simply TM it to flying. Still the best.

Kyogre- only thing that comes close in the future is Palkia but as it stands Kyogre is stupidly strong and probably tied with mewtwo as the best pokemon in the pokemon go to be honest (factoring bulk, typing, attack and effectiveness profile)

Mewtwo- best psychic of all generations, essentially a risk-free investment. The only cost you have to factor in is any lost opportunity if you needed the dust/rare candy elsewhere.

Groundon- see mewtwo.

Raikou has enjoyed heavy use, being uncontested as best counter for Kyogre and Lugia, was even super competitive vs Ho-Oh. However yes it is not as useful now.

The fire types will be good vs the Titans but we do not know for sure if they are dropping yet (though it is an educated guess)

Rayquaza as others have said. That would be the best one that will keep giving generations to come. Mewtwo because I’m sure they will change his move sets soon once he (if ever) rotates out, and give you more options in the future. Groudon and kyogre will be the best at what they do. The nerf to palkia we will have to see but I doubt they will give it a double water move set. Gen 5 will bring the best fire, ice, and lightning attackers to date with their dragons so that will be something to look forward to, and something else Rayquaza will help with.

Let's organize it by these categories:
1) Meta Usage
2) Type Supremacy/Future Proofing
3) Generalist Use
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1) Current Raid Bosses are (Valuable group bosses) Latis, TTar, Absol, Aggron, and (Soloable tier 3s) Granbull, Jynx, Piloswine, Gengar, Machamp. Gyms are still filled with Blissey, Chansey, Snorlax, and Slaking, with the still-prevalent Dragonite and the occasional Tyranitar.

1) Rayquaza: Definitely the current winner, here. Strong 2-bar for gym clearing with the neutral-power of Dragon-type effectiveness. Highest-damage option for Latis and lots of power against Machamp and gym Dragonites. Weakness to Dragon-moves from Latis and Dragonite, and doesn't stand up at all to Jynx, Piloswine, and Granbull.

2) Mewtwo: Another great option against Latis, and a powered up one practically guarantees victory against Gengar and Machamp solos. Has the added bonus of resisting Psychic moves from Latis, though is a bit frail against Solarbeam, as well as Gengars super-effective Ghost moves. Is great for general gym clearing with strong moves and the great coverage of Ghost-type, but is somewhat underwhelming against the Normal and Dark-type gym defense stars when not carrying Focus Blast.

3) Latios: What...? Yeah, actually a very good option against Latios/Latias, especially because it resists the Psychic sets as well as Solarbeam and Thunder. Great for dodging, and the three-bar Dragon Claw has great type and neutral coverage in gyms, great against low-motivation gyms. Isn't terrible against Dragons because you can dodge, but watch out for the Dodge-Bug in larger raid groups, which occurs when a move would be fatal if not dodged. Not that it's a common sight, but look out for Gardevoir in gyms. Latios, despite its legendary status, quivers to it.

4) Groudon/Kyogre: While lacking a serious niche in the current raid scene, they perform well in gyms when they are weather-boosted. Their drawback is having access to only 1-bar Charged Moves, but they are not weak to moves commonly seen in gyms, and are even relatively potion-efficient when one considers their massive Defense stat and Groudon's ability to dodge with Mud Shot.

5) Latias: A bulky Latios with a Charged Move better suited for raw power than for dodging. Same as above, in that it is good for gym sweeping and great for countering the Latis, though you cannot expect to dodge the super-effective Dragon Moves while using Outrage like you can with Latios. Though lower in DPS (And thus facing competition from Dragonite and Salamence), you can expect to survive despite the dodge-glitch for longer due to the added bulk.

6) Mew: No way...yes. For the current Legendaries, Mew makes waves with its possible Quick Moves Shadow Claw and Dragon Tail, which are super-effective as well as some of the best Quick Moves in the game in a vacuum (despite not receiving STAB). Mew works well with Ice Beam, Dazzling Gleam, Blizzard, and Dragon Claw against the Latis, carrying bulk and also with the nice bonus of resisting Psychic sets.

7) Lugia: Dragon Tail provides some super-effectiveness without having to open yourself to the weakness of Dragon-Types, and it comes bundled with resistance to Psychic sets and Solarbeam against Latios (though weak to Thunder, it is a weak move still). Make use of Sky Attack's buff, as it is a great move and easy to dodge with. It is a godsend for Machamp solos and even a decent bulk option for Gengar solos with a Psychic set when Gengar is carrying Focus Blast. It is a surprisingly good option for gyms if you are a little patient, as it is unlikely to faint and the most potion-efficient mon in the game with the bonus of having very good moves too (while mons like Tyranitar are great but have poor move choices).

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2) This section compares Pokemon to their type-competition as well as future obsolescence:

1) Groudon: Will not be replaced by a legendary species, period. Rhyperior may come close to it in terms of bulk but that's it, and this depends on the moves it receives (and it may receive Smack Down yet, which is a Rock-type move). Ground is a very good move type in terms of viable targets, and is the best option against targets with Double Weaknesses like Magneton. Additionally, it is the only type that can stand up to Electric. Currently, Rhydon doesn't even hold a candle to Groudon, and this is the current best competitor.

2) Kyogre: Slightly threatened potentially by Palkia in the future but that's it, and this depends on moves too, as Palkia is also a Dragon-type. Palkia's typing would be better for dealing with Fire types and would also shrug off its weakness to Electric. However, were I a betting man, at least one of Palkia's Quick Moves would probably be Dragon Tail unless the moves are changed by Gen 4. Gyarados comes somewhat close to Kyogre (more than Rhydon to Groudon) but Kyogre is still the clear general winner, with more damage than Gyarados and more bulk than Vaporeon/Milotic. Gyarados, it should be noted, has a double-resistance to Ground, which is a common favorite target of Water-types.

3) Raikou: Potentially threatened by Zekrom, a gen V Dragon-type, but that's about it. Zekrom is weak to Ice attacks, commonly carried by Water-type targets of Electric. Zekrom will likely have higher stats than Raikou, but it also depends on moves. Though Zekrom is also a Dragon-Type, I'm betting it gets at least one Electric Move. Raikou faces competition from fellow Legendary Zapdos, but has the edge because its current moves are better and it isn't weak to Ice and because it resists Electric. Zapdos, however, sometimes pulls ahead against targets carrying Ground or Grass moves.

4) Zapdos: See above. Zapdos has lower stats but higher attack and a different sub-typing that harms or helps depending on the matchup. Currently outpaced due to a slightly worse movepool but that may change.

5) Mewtwo: Mewtwo has insanely high stats and phenomenal attack but also faces serious competition as Psychic is a favorite type of legendaries, it seems. Outdamaged by Deoxys but its frailty and movepool is a joke. Looking ahead, it is approached in damage closely by Azelf and Lunala but never surpassed. Lunala may give it bulk to stand up to Mewtwo. Mewtwo's current problem, though, is the lack of a powerful Psychic-type move, so future Psychics may give it a run for its money. It, then, faces Ghost-type competition from Giratina and Lunala. Currently, it obliterates any other Psychic type for damage. Lugia is its only true rival as Lugia carries unheard of bulk and better Psychic moves. Latios has decent damage and bulk but a poor movepool, and Latias carries some bulk but an equally poor Psychic movepool. Mewtwo's Confusion is at least better than the Latis' Zen Headbutt.

6) Moltres: Has the best Fire-Moves and a typing that is well-suited for Grass and Bug targets but poor against Ice targets. Faces slight DPS competition from Blast Burn Charizard but is clearly superior to any other nonlegendary Fire-type such as Flareon. Entei has more bulk and access to an (bad) 2-bar. Doesn't matter - Reshiram will blow it away in the distant future, and it faces competition from that fairy/fire thing in gen-whatever.

7) Entei: I don't like Entei at all, personally. It has bulk but is outDPSed even by Flareon. Not getting any of my rare candies. A better general option against Ice-types than Moltres while also resisting ice-moves, which rock and fighting types cannot do (and current Steel types are weak). Reshiram will annihilate this one too but by a far larger margin.

8) Rayquaza: The best Dragon currently but only by a little. Already barely keeping its head above the clouds of non-legendaries, and it already faces dodging-competition from Latios. An army of Dragons is coming for the Sky Throne, as Dragons seem to be a favored type for legendaries. Palkia, Dialga, Giratina, Kyurem, Reshiram, Zekrom, and Zygarde all carry high enough stats to threaten it. Though in some cases it may have a slight DPS advantage to these depending on movesets, its bulk is somewhat lackluster and it carries double-weakness to ice. All of these 'mons will have a lot more bulk, and any people I've talked to haven't rare-candied their Rayquaza when they have heaps of free Dratini candy to get an only slightly-worse option.

9) Articuno: This one's an interesting one for me. Though Regice will not outdamage Articuno, it carries much more bulk and has virtually-useless subtyping. Articuno already faces DPS competition from Jynx, who outpaces it and has better moves but is far more frail. Weavile and Glaceon may give it a run for its money, and that's to say nothing of what legendary Kyurem will do to it.

10) Ho-Oh: No-Oh

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3) Outside of specialized matchup, legendaries are great because, well, they vastly outperform most non-legendaries. Generalist use will look at overall gym use as well as raid use against nonspecialized targets.

1) Rayquaza: Best current generalist, slightly outpacing Mewtwo. Rayquaza's moves have far better type coverage (only resisted by Steel and Fairy) and are even effective against Dragons to boot. Much faster Quick Move but a slower Charged Move with a very late damage window. At least it hits those fat normal types in gyms. Also has lots of very good resistances and a few good double-resistances.

2) Mewtwo: The next-best generalist. It's hard to get because it's EXclusive, but it's also been out longer than any legendary. Mewtwo's highest damage set is its Shadow Ball set, meaning it covers two types but is master of neither. Not that it matters though, as it performs both duties admirably. Great for filling holes in raid teams too - though it takes high damage from a usual lack of resistances, this is good for machinegunning Shadow Balls off. Shadow Ball has great coverage for raids but poor coverage for gyms against common Normal-type defenders. Some trainers use a Focus Blast Mewtwo for gyms. Best of all, Mewtwo has two good Quick Move options suited for DPS or dodging playstyles.

3) Groudon/Kyogre: Fantastic generalists in their own right, though they may find some of their moves resisted. Very potion-efficient, and are fantastic when weather-boosted (Groudon, for me in SoCal, is almost always boosted), making them sort of "regional" bests depending on the most common weather of your local region. Problem with gym sweeping is they only have access to 1-bars.

4) Lugia: Has several good move options - basically anything but Hydro Pump, though I'm partial to Dragon Tail/Sky Attack and Extrasensory/Sky Attack. Sky Attack is the best Charged Move by far, and Dragon Tail has coverage and Extrasensory has great energy buildup and STAB. Very potion efficient and its damage is nothing to sneeze at.

5) Ho-Oh: A "lesser-Lugia" with more diverse moves but none of them are really any good, and a lot of them lack STAB too. Its Quick Moves are high-tier ones in a vacuum but without STAB are somewhat lackluster.

6) Latios: Good general option with great coverage and two good move combinations: Dragon set and psychic set. The Dragon one is far superior, and has access to a good, dodge-friendly legacy set. Dragons as generalists face lots of competition from the psuedos.

7) Latias: I guess if you need bulk and like dodging but not for the Charged Move?

8) Moltres: When weather-boosted, is a very high-damage option that can beat out even Dragonite.

9) Raikou: Decent as a generalist, and many are a fan of the high-energy and dodge-friendly Thundershock/Wild Charge combination. Wild Charge is great because its fast, high-damage, and 2-bar, but Rainy weather can be rare depending on location and, as a generalist, it is slightly below Dragonite.

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I hope this helped!

The weather trio.