Suggestion: if possible, why not make one of the forests include a mazelike section with lots of trainers, berries, and hidden items hidden in it? It would make it so that you could entice them into going in there, without forcing them (as forcing them to do an insanely difficult maze just to get from one town to another would put them off the game) as well as enabling you to put grass all over the place for random battles, while still having spots to rest in that a cave wouldn't offer (since you can get a fight anywhere in there).
It would also allow you to, say, put in hidden areas that only persistent players would find? Say put the entrance to the second forest hidden inside the first forest (to represent going deeper) and then further into the deep, mazelike region, have caves with their own special things? say have several caves and a specific pokémon can only be found in one of them, and only rarely at that...
Oh man... the whiners who weren't smart enough to tell that was an ALPHA would probably never finish the Pokédex, but people who love the game would enjoy the challenge! (Think along the lines of how rewarding it is to finaly catch a Feebas)
those are some nice idea's you got there, some are already implemented, some i will now implement thanks to your suggestions and some i'm going to ignore. What is what? wait and see.