I don't see what it would hurt. If you don't want to use them then simply don't evolve your pokemon. It would add to the game, IMO. It would make several of the gym leaders and Elite 4 members tougher. Pryce was the 7th gym leader, I think he should have something with the power of Mamoswine as his main pokemon rather than Piloswine, for example.
In my opinion, the Kanto pokemon didn't only overshadow in the anime but they did in the game too.
Like Pidgey, Hoothoot was the regional bird of Johto but players had the option of taking Pidgey again instead. It just kinda feels like the game was to clustered. You couldn't even catch certain Johto pokemon until you had already beaten the Elite 4. What if I want to train a Larvitar or Sneasle and use it during the majority of the game?
Anyway, especially since the game had the player go back to Kanto after defeating the Elite 4, I don't see why they pushed the Kanto pokemon on us during Johto. The ones that are found every where are understandable, like Magikarp and Geodude, but Growlithe rather than Houndour? Pidgey stealing Hoothoot's region?
I'd love to see the pokedex handled the way it was in Platinum. Every second generation pokemon on the JohtoDex and a handful of pokemon from the other three regions added in for good measure. After defeating the Elite 4 players would get the NationalDex and travel to Kanto where they could collect the remaining Kanto critters. Something like the PokeRadar and Swarms can be added for the player to catch the Hoeen and Sinnoh pokemon, there are two regions so there would be plenty of space to put them all.