Generations is probably going with the male protagonists because they've been featured the least for animation, and Red and Gold/Ethan appear in more games than Blue/Leaf, Kris, or Lyra. Still though, it doesn't explain why Lucas and Dawn weren't shown, or Nate and Rosa. It's still interesting that we have some major choices shown though.
Red - Bulbasaur and Green - Blastoise
Brendan - Sceptile meaning May - Blaziken
Generation V - White and White 2