I posted a few ideas some pages back but I've thought of a couple more! These are all personal desires and might not be entirely feasible but hey, I can dream can't I?
* A more interactive/customisable touch screen - I'd love to be able to add my own icons to the bottom touch screen for ease of use as you can on a iPhone/smart phone. I like having 'registered' functions you can access quickly by pressing the Y button but a personalised icon screen would be a lot easier and fun to use. For example, there could be 3 rows of 4 icons. The top row could be defaulted to Pokemon, Bag, Options and Save and then you could customise the remaining 2 rows to show whatever you wish. It would be neat to have a shortcut to things you personally use a lot of such as the Dowsing Machine, Map, and Bicycle available with one tap of the touch screen. Perhaps some people would like to create a 'Surf' or 'Fly' icon so you just have to tap it to activate the action rather than pressing X > Pokemon > Select Pokemon > Fly/Surf or a C-Gear icon. Either way it would allow players to create their own ideal mixture of most commonly used items and functions.
* Random weather changes dependant on seasons - This would be great. It would give the whole game a more natural, realistic feel. Perhaps there could be a 25% chance of routes and towns being engulfed in hail or snow during winter instead of one specific route always displaying the same weather effects that disappear as soon as you reach the next area.
* Different ways to attract and find previous Gen Pokemon - Searching grass and fishing are fine but I think it would be fun to introduce some other ways to find specific Pokemon after you've completed the game and explored the region. For example to find a certain types of Bird Pokemon, you would have to use Bird Whistles (or PokeWhistles, whatever they want to call it) and play certain tunes in order to lure the birds from the sky or trees. Other methods could include laying nets/traps to which you would have to set up and return to later, like you do with slathering honey to trees.