If we remove trainers on Route 202, then we have two entire routes without any real battles. That isn't really a great way to start a game. If anything, we want to leave them on 202 and remove them from 203. However, we may not need to do anything so dramatic: I remember great frustration trying to beat that stupid Onix with Pikachu or Charmander. Brock was actually one of the hardest gym leaders for me!

On to the second issue...
The 12th gym leader has pokemon in the low 70s. In order to get that high, I'll probably have to run through a load of tall grass. Usually, I can (barely) manage the gyms through a combination of facing every trainer on the way, a lot of revives, and pure dumb luck. That's my pokemon strategy. I don't think Caldera/Kirant are that much larger than Hoenn (but I could be wrong). So, it's reasonable to assume that, if I were to use my usual strategy, I'd start to fail somewhere around leader 6 (I usually get to the E4 with levels in the low to mid 40s). I think we may need to decrease gym leader levels. A lot of the gym leaders won't have more than a short route separating them from somewhere you've already been, and it's difficult to fit a bunch of trainers there. So, I think that "approaching 100" may be a huge overestimation.
There's also an advantage to pokemon who could have evolved; they get better moves faster.

These issues are really things that needs to be playtested to make an accurate prediction. Once the demo is released, we'll be able to get feedback about what needs to be changed to improve the game. After that, I guess we'll need some sort of alpha/beta testing system and adjust according to that.

For now, we can try to deal with that first situation.