Electric King? / Or why Raikou is still the best

While your overall point is fine.

When you do analysis, you can't only focus on points that support you, and not ones that dont.

For example: You can't bring up Zapados second type flying giving it an ice weakness as a con against water types, and not bring up Magnezone's second type steel giving it a resist against water types.

To Niantic's credit, the one thing they have done is keep all the pokemon relatively close. I don't think you can really go wrong with either of those electric types. I am looking forward to Magnezone because of the main series games, I will probably max one out. I also love Jolteon because of discharge. And I have a level 40 Zapdos, the reason I chose Instinct. Sure it has charge beam, but it isn't completely out clasped. There isn't enough to really fuss over. Even if I don't max a Magnezone, my level 40 Zapdos and Jolteon are more than enough to get the job done. Then you add I have a level 40 100% Raichu to add to my electric group.

Pokebattler currently ranks TS/TB Zapdos and TS/ZC Zapdos ahead of TS/WC Raikou as a Lugia counter (using time to win as the criterion). My own CDPS calculations indicate that TS helps Zappy close the gap, reducing the difference in DPS by about 2/3. But what's most important to me is that:

1) Right now I have no powered up Zapdos, and 35 Zapdos candy.

2) Right now I have no Raikou at all.

3) Given double candy this weekend, I can go out and catch 10-25 Zapdos, gaining 60-150 candy (6/catch), at level 20 (or 25 if it's rainy or windy), and get 2-4 really strong Zapdos from that. This is a clear win for me, regardless of whether Raikou with Wild Charge is better or not.

All that said, I think Zapdos with TS/TB, TS/ZC, and Raikou with Ts?WC are all really good and will be competetive for a long time. Who is the very best is not that important to me, just that they are all really good and really close.

Finally, the good thing about Zapdos's flying typing is that it takes away the weakness to Ground, replacing it with resistance, and adds several other good resistances. Rock is the key weakness added, then ice. Which, to me, just means that Zapdos and Raikou are different, which is a good thing - have some of each, and use as appropriate. Going against a water pokemon with a secondary ground attack, Zappy is your guy. Going against water with a secondary Ice attack, Raikou is the way to go. Neither better or worse there, just different.

Whether or not a Pokemon can learn a move "naturally" is no indicator on if they'll get it in PoGo, Salamence being a prime example of this as none of the moves it learns are level-up (inb4 Fire Fang, in every instance you need a Heart Scale to teach it that. Dragon Tail requires the same or a TM).

I don't think Raikou will straight up lose the throne, rather I think there are select instances where using the alternatives may be more favorable. Electivire with TS/WC will have slightly more DPS than Raikou but with significantly less bulk it put out noticeably less damage. Magnezone's secondary type gives it some situations where it stands to be more favorable (Blizzard Kyogre possibly?). Zapdos getting TS helps bridge the gap between it and Raikou but with a secondary type that's more harmful than helpful and less bulk overall it ends up being 2nd place in many matchups.

I think overall Raikou will still come out on top, though there are likely to be special cases where another attacker would be preferred.

I think it doesn't matter overmuch, because gen 4 doesn't have any legendaries weak to electric. It's not worth powering legendaries if all we get for targets are short reruns like Zapdos day. You'll probably do fine with Electivires or Magnezones until Zekrom comes in gen 5.

Better put those precious rare candies into legendaries who have relevant matchups, like Rayquaza, Groudon and Kyogre.