While I don't expect each game to have it's own region or anything, I would like it if each game had you start at opposite sides of the world. (E.G, X starts in the North, whereas Y starts in the south) Although pokemon in each game are at around the same places, the levels they are at differ wildly in relation to how far the area is in the respective game. The story is basically the same in both of course, but with different locations for certain events, maybe a few different events, and maybe a few events have different rewards to coincide with when they happen (E.G, the dark Gym leader has a job for you. He's leader 7 in X, and 2 in Y, so in Y The reward is the bike, whereas in X it's HM 06 Or so, as you already got the bike around the second Gym.
Would bring diversity to the games, and offer two half unique regions with a lot less work.
But there's still tomorrow Forget the sorrow And I can be on the Last Train Home Watch it pass the day As it fades away No more time to care No more time Today
I don't know about item differences either. I prefer superficial, cosmetic differences. For example, in Black and White, Drayden was the gym leader in Black, but it was Iris in White. In Black 2 I got the Water Reversal Cave whereas White 2 players got the Lava Reversal Cave. Those sorts of differences are cool. I liked picking which cave I liked better through screenshots, and which Route 4 I preferred, and which cover legendary. Altering the game play experience completely by denying one side an HM or Key Item at a certain point seems like it would just be aggrevating. I don't want to have to pick whether I want access to the Super Rod pre or post Elite 4, or have access to Waterfall instead. It seems like it would fundamentally inhibit your experience.