I'm having a hard time deciding and just had to vote for two.
Squirtle is pretty awesome with its shell and being a cute turtle and fairly basic in its design, which is something I appreciate. In-game, I never used it much though, except on Yellow version. Its evolutions keep the same feeling, imo, Wartortle being a fav middle evo.
Piplup, I hardly ever used in the games or anywhere really. but I appreciate its design and later its typing. Piplup is cute enough, Prinplup is a bit boring - but Empoleon makes up for it. Sure, it's a bit weirdly bulky but it works well and it having steel wings as weapons is pretty darn cool. I still think it would have been a cool thing if it was water/ice though. Since it's a penguin. It could have had ice shards emerging to line its wings and act as scythes.
Seems like Mudkip and Piplup are winning, looking at the poll :]
The others, I don't care as much for, even though I love Totodile's design and Dewott's everything pretty much. I don't like the other pokémon in those lives though. And Mudkip, I don't really like at all, except for in Hoenn games where I use it almost all the time xD But still, its design freaks me out too much. Just eww. *isn't bashing, just telling* :]
Froakie, I like. If his evolutions are anything close to this, he might end up my fav starter in gen VI.