On Fire Red/Leaf Green it always comes down to Squirtle because of Blaistoise., as he is the hardest Pokemon to replace in the game. Charizard, for simple power can be replaced with Moltres, while Venesaur is actually harder to replace, I rarely have a grass Pokemon in my final team.
With RS/E I was not to big of a fan of the final Evolutions of the starters, so I generally tried to find Pokemon throughout the game to replace the starters with, but I always chose Torchic until I could replace it.