Dang that's a good lineup.
- I would suggest TMing your top TTar to Crunch. You already have one with SE and there are other options for Rock, yet TTar is the definitive answer to Dark-type power.
- Consider bringing your Raikou to level 30 if not maxing it. Level 30 makes a good cutoff since costs raise exponentially after that and CP bonuses are cut in half after 30. It's the best current Electric-type in the game, a decent generalist, and is unlikely to be replaced.
- Kyogre is well worth investment because it is the same stats as Groudon but with a superior moveset for neutral situations - and Water is a very useful type to have for specializing too.
- Mewtwo is always worth investment since it's the premier generalist as well as a Psychic/Ghost specialist. You could consider FTMing to Confusion/Shadow Ball for a DPS gain but I don't think this is necessary. Psycho Cut is better when used against specialist targets such as Gengar and Alakazam, and is also better-suited for dodging.
- I wouldn't invest in Rhydon right now. It's good as is (with the right moveset, too) but can be caught at very high levels wild. The other day I evolved one to well over 3,000 CP wild-caught.
End-all, if you have a lot of stardust but are short on rare candies (since most of the options I advised are legendaries), TTar tops the list for being worth stardust investment. Candies are definitely not easy to come by, but it makes a great walkin' buddy. Gyarados is another decent option, and Dragonite could be considered too - though your having a Mewtwo somewhat mitigates your need for powerful generalists.