While my favorite starter actually comes from the Sinnoh region (Empoleon), I truly think that the Hoenn starters as a whole were the best. In my two main playthroughs of Sapphire, both Swampert and Sceptile were key components on my team, and 2 out of maybe 5 starters that I kept on my team through the entire game. And even though I haven't really used Blaziken, I do know it's consider one of the best starters, thanks to its Speed Boost ability and good movepool.
After that, I would then have to rank the groups of starters as Sinnoh (all have dual-typings, and it includes my favorite starter), Kanto (tough to have the original three drop any lower than third), Unova (I've used these starters more than the Kanto ones, but I don't like them quite as much), and Johto (never found much appealing about Johto's starters). I don't know where Kalos' starters rank quite yet, considering we haven't even seen their evolutions at this point.