I'm a big Poke-fan, and I've pumped in hundreds of hours over the years to both the portable and console games featuring these creatures.
But the "Two Versions of the same game" theme has always bugged me. It's kinda lame that the only differences between two versions is that they have a few exclusive Pokemon. That was okay for Red and Blue, but it's getting kind of old. Granted, R/S put in different baddies, but that still isn't enough. I think Nintendo needs to raise the stakes more for the next generation...
*Different Pokemon/Baddies - They've already done this, so I'm not going to get into these.
*Different main characters - The option to choose a male or female character is great, but an even better option is to have each version have completely different male and female characters. Perhaps even have one version with older looking characters, to appeal to us who have been with the series since 1998.
* Different layouts - The layout of the game would be completely different from one version to the next, a completely different land.
* Different Gyms - Here's a biggie... have each game have exclusive gyms and gym leaders. You can even use the wireless link to jump into another version, challenge the gym leader and get that badge added to your collection as well!
* Different side quests and mini-games - Perhaps in one version you have to escape a sinking ship while fighting off a bunch of Gyarados, while in the other version you have to solve a dungeon puzzle. On a side note of that, I'd like to see puzzles that incorperate your Pokemon. Like a door that's on fire, you'd need to have a Water Pokemon that knows a water type attack to get by.
That's all I can think of at the moment, but feel free to add some more!