You could still essentially go anywhere you wanted right off the bat aside from Cinnabar, Pallet and Pewter -- and even then as soon as you'd done the missing part sidequest you could go there as you pleased.
This is what I really love about the Johto games. The incredible free-roaming in the aftergame.
Oh, well I guess my idea could still work. Also there's places off-route that maybe they could have put higher leveled Pokemon, places you're not required to go to. It maybe a bit more chaotic way of level progression but as soon as your Pokemon are up to level it would cease to be a problem.
I wonder if GameFreak will ever try a freeroaming region. They let us now battle the Elite Four in whatever order we like (except in ORAS but that was for nostalgia sake... and I do think they should have let us battle them in any order). They can make the main routes connecting the cities/towns to one another at first but as you get badges (and thus HMs) you'll be able to access new areas which is how they can handle the story. But this is getting off topic, so I'll counteract it here's a new annoyance:
Trading Shards for evolution stones. As you may recall, you can trade the Red, Blue, Yellow, and Green Shards for a Fire, Water, Thunder, or Leaf Stone. But that's all, there's no way to trade for a Moon, Sun, Shiny, Dusk, or Dawn Stone. Being this was around the time you should start having a full party, having him able to give out those stones would have helped those with Pokemon that evolve that way be able to evolve. If they didn't want to introduce new items to trade them for they could have made you trade them for other existing item (and hint you can use these items for that purpose early on so you don't accidentally sell them). Like Pearl = Moon, Nugget = Sun, Star Piece = Shiny, Rare Bone = Dusk, Pretty Wing = Dawn. Or how about letting us choose which stone we want, why make them color dependent (well, besides justifying there being four colored shards)?