Kanto - Charmander
I'm pretty torn here. I'd like to say Bulbasaur since it's such a great help through the first part of the game, though that's mostly due to its typing advantage against the two first gyms, while Charmander and its evolutions have great moves, great stats as far as I remember, and is a fan favourite, though I honestly have more experiences with Bulbasaur's line. I guess I'd have to say Charmander due to most other people feeling that way, and I know it isn't bad.
Johto - Totodile
Not much to discuss here really. Chikorita has a great design and all, but as a Pokémon, and especially as a starter, it isn't really much of a help, especially considering it's weak against the first two gyms in the game. Cyndaquil's line is also pretty strong, the help it gives you in the game is pretty equal to what Totodile's line give you, and it's also the one I've used the most of the three, however out of the two, though I'm choosing Totodile, just because it's the superior of the two, mainly due to the typing advantage, so yeah.
Hoenn - Mudkip
This is probably the hardest line of starters to choose between, mainly because they're all pretty darn amazing and probably the best starters there is. One thing is for sure though here, in my opinion Treecko comes dead last. I love it and all, but it isn't much help as a main team Pokémon towards the end of the games. It's super fast, and that's great, however I feel like that's the only thing I can really rely on it with. The only move which it learns by leveling up which I feel is useful is Leaf Blade, and otherwise it just isn't really good. Torchic's line isn't really that good in the beginning, however what makes it so great is its great stats, and the fact that it's a Fire/Fighting Pokémon (even though we see that like every generation from now on), and definitely a favourite between many, however it isn't really that helpful before you come closer to the end in my experience. Mudkip's line, however, is pretty darn amazing throughout the whole adventure. I mean, of course it isn't that super good in the beginning when it's only a Mudkip, but in case you haven't evolved it by the first gym, it has a type advantage, and from when it evolves, it is just beast. Due to its unique typing, it isn't weak to that many typings, as well as strong to quite a few, there isn't any gym in the region which it is weak to, iirc it has the highest base stats of any non-legendary and non-pseudo-legendary Pokémon in its final evolution, so definitely not slobby on that part, and is just pretty darn amazing. So first definitely goes to Mudkip.
Sinnoh - Chimchar
Pretty self-explanatory. Apart from being the only Fire type Pokémon available apart from Ponyta and Rapidash, which aren't really good, it's also the strongest of the 3 starters. It has the most useful typing, as well as a great movepool. I find it hard comparing it to the other two because they're all pretty unique in their own way, however it's the best choice of a starter in that region, so definitely my choice of the best.
Unova - Oshawott
I have no idea what I'm talking about with Unova. Never played the games, so I'm just copying off what most other people said, as well as I definitely wouldn't say another Fire/Fighting starter >:(