The only real problem I had with the game was that it is way too short. There's only 3 cities to visit after the E4. I prefer the days of playing Pokemon Gold, Silver & Crystas on my Gameboy Color 'cause you get to go to Kanto after the E4 and there's 16 gyms. Pokemon D/P & B/W is really lacking...
I agree that the game is far too linear and should have more obstacles, the only trouble I ever had was with the quicksand. I had to look up on Google to find out how to get past it. I felt stupid when I found out that I just have to walk around the edges :P