I'm gonna try answer this question as best I can... xD
The Pokemon that have the highest stats in every game are probably the stronger ones. Since we don't know what the exact stats of the strongest trainers are (unless we don't know and it's hidden in the coding somewhere) then there is a good chance that Red in HGSS has the highest statted Pokemon. It's a good guess, since his Pokemon's stats would have matured the most out of all since he does have the strongest Pokemon in any of the games.
Most Gen I Pokemon are available in every game, notably Geodude. However, this becomes a little hard since Gen 5, Black and White, features no Pokemon from other generations Pre-National Dex. And Post-National Dex there is only a handful. In one way or another, I guess I could promise Magikarp. Otherwise, I don't think there are many. But, trust me, there are some.
It should also be noted that in Ruby, Sapphire, Emerald, FireRed and LeafGreen some of the Johto Pokemon are unavailable. Of course, there are plenty of games that are available in the 3rd Generation that I'm sure house all of the Johto Pokemon, but otherwise there is no way for those games to get all of the Gen II Pokemon.
Hope I helped. :)