Hmm, well truthfully Totodile, Mudkip, and Squirtle logically have the same habitat requirements so I would think them all being on the same general area would make sense. Having all three on route 119 or perhaps split between routes 118, 119, and parts of 120 would make sense. I say this since crocodiles (actual crocodiles I mean) can traverse both saltwater and freshwater so seeing totodile on the sea route on 118 in either the grass or the water could be logical. Mudkip would like the conditions of 119, and Squirtle would like the lakeshore areas of 120.
As for any of the fire starters, I would have expected Charmander at Mt. Chimney along Jagged Pass or the Fiery Path. Cyndaquil meanwhile I believe would make more sense on the daycare center route. Torchic I believe might be fine as is.
As fr the grass starters, the idea of Treecko being in Petalburg Woods would be a nice nod to the anime, as thats where Ash got his. Bulbasaur could work anyplace in Hoenn that has enough plants to satisfy its needs, not just the woods, but I think Route 114 might work well since its near Meteor Falls and Bulbasaur's line have more in common with some prehistoric mammal like reptiles than they do with frogs and toads as their appearance would suggest making the proximity to a dragon habitat a little more logical in turn. Chikorita meanwhile might be perfect for Route 110 since its a wide open route and the exposure to the sun would be perfect for them there.
EDIT: Oh this is something I forgot to mention in my post but I'll edit it in here; if at all possible I recommend you add a few more moves as I remembered that Meditite/Medicham and some other pokemon lack th emoves to make use of their typing even taking into account the PSS in this game. Unless you added some 4th or 5th/6th gen moves into the game, pokemon such as Meditite, Absol, and others will be lacking a key move in their arsenal. Meditite with Zen Headbutt or Psycho Cutter for example, plus Absol gets Psycho Cutter too. I would suggest changing the type of a move like Secret Power to Psychic while keeping it Physical but I dunno if that ruins the vanilla feel of the game considering.