Random weather effects, and not just in battle. Imagine walking down a nice, sunny route. It gradually gets darker and darker, and all of a sudden, the entire screen flashes white for a split second, and you hear the crash of thunder a couple seconds later. Right after that, it starts pouring down rain. Would be friggen' epic imo. It should have storms, blizzards, hail, fog (not as dense in DPPt, you would still be able to see), maybe even something like a tornado could rarely happen!
I would also like to see seasonal changes. I liked some other guys idea about having pokemon migrate throughout the seasons. It wouldn't limit certain pokemon to only be able to be found in certain changes, but would change their locations, and have cool aesthetic effects. if the cycles were only like a day or two though, I can see pokemon only being able to be found in the winter or summer being available. They could also throw in a pokemon like castform that changes depending on the season!