Some of the games I've only played once, so that's why my percentage is at 100% (even though I might choose a different starter the second time around).
Kanto
Bulbasaur 33%, Charmander 67%, Squirtle 0%
Growing up, it felt wrong not to take Charmander and have it evolve into an awesome Charizard. One of the more recent times I played, though, I started with Bulbasaur, but I found I didn't enjoy my playthrough quite as much. And I've always liked Squirtle, so I'm not sure why I've never used it.
Johto
Chikorita 33%, Cyndaquil 33%, Totodile 33%
Of the 3 main runs I can remember playing in Johto-based games, I had no particular preference towards my starter Pokemon. All 3 of them stayed on my team for the majority of the game, but they all ended up taking a back seat to my other Pokemon.
Hoenn
Treecko 50%, Torchic 0%, Mudkip 50%
While these numbers looked like I favored Treecko and Mudkip equally, my Sceptile ended up being my best Pokemon in Sapphire, and I still have my original one from 9 years ago on my current HeartGold.
Sinnoh
Turtwig 0%, Chimchar 0%, Piplup 100%
One of the regions where the numbers are stacked in favor of one Pokemon due to only one playthrough. However, my Empoleon became a powerhouse on my team, and I really liked the Water/Steel typing, so I would probably choose Piplup again if I ever went back for another run.
Unova
Snivy 0%, Tepig 0%, Oshawott 100%
And the other region with a skewed number. My Oshawott -> Samurott didn't play as big of a role on my team as I was expecting, but it held it's own. When I get B/W2, I'm leaning towards choosing Tepig as my starter, but I'm not fully decided yet.