For the great and ultra leagues, at 1500CP and 2500CP limits, the best pokemon should come down to 3 things:
1. Typing
2. Moveset
3. Synergy
Typing will be important, as some types are simply superior to others, especially some dual-types. Picking pokemon that have few weaknesses should make your team a lot stronger. This is a tough one, as the important types to pick will likely depend on which pokemon are viewed as strongest.
Moveset is the easiest by far. We currently know the best 4 charge moves in the game: Hydro Cannon, Meteor Mash, Frenzy Plant, and Blast Burn. I think we can agree that Venusaur is superior to Meganium, however it's harder to argue for Charizard over Typhlosion (Charizard has a better fast move, but Typhlosion has better typing - Charizards dual typing will expose him to more weaknesses and to a double weakness).
Beyond these 4 (moves, 5 pokemon) - what other picks are destined for greatness? I believe Sky Attack is the strongest non-exclusive charge move. Molters is likely already outclassed by Charizard, but does Lugia enter as a threat? It should be noted that Lugia could appear in the 2500CP draw, but it's impossible to get a 1500CP Lugia.
Is Shadow Ball one of the next strongest moves? Is Gengar ideal at 1500 and 2500CP, or are there Ghosts with preferable stat distributions?
What other moves come to mind?
