If, as many have assumed, it's possible that this generation could introduce 3D battles to the handheld games, then the possibilities suddenly are endless! Here's a few ideas:
First off, there's the possibility that Speed may become an even MORE powerful stat. If battles take place in real-time, it might be impossible to predict what might happen, as the abilities of Pokemon will suddenly matter much less, as mobility will take the forefront. In other words, the Pokemon that most effortlessly traverse the map and avoid attacks (or just carpet bomb the battlefield) would be the dominant types. An example of a game somewhat like this would be Nintendo's Custom Robo games. And obviously, if the battlefield takes a turn for the tactical (like EvilMario suggested), 6vs6 battles could easily turn into TRUE 6vs6 combat, instead of a party of 6 fighting one or two at a time.
edit: Check out BoyBoy's post above for possible balance issues!
Or perhaps that's too extreme for the DS, hmm? Too much processing power and memory. Okay then, what about something closer to Final Fantasy's Active Time Battle System: each Pokemon has a "gauge" that fills up faster as the Speed stat grows. This would allow, say, extremely fast Pokemon like Jolteon to attack twice as often as Pokemon like Golem. Now, in the world of Pokemon, where battles are decided so quickly, perhaps this system would not be ideal. Slow Pokemon would essentially become obsolete in some cases. For instance, what's the point in having huge defenses like Shuckle if Aerodactyl can attack you 3-4 times before you even move, etc.? But that's not to say something LIKE that could be balanced out for the Pokemon world.
But, if they're going to allow you to at least TRADE with Gen 4 at some point (likely), then any drastic battle system changes need to make sense in the context of the stat system we currently have. Thus, I'm not expecting any drastic changes beyond what we are used to: new attacks, abilities and Pokemon will alter the balance while ONE OR TWO new aspects (hold item, ability, physical/special) will redefine how our games are played. It's hard to pin down possibilities for things on par with hold items, abilities or physical/special moves, as such things are so multi-dimensional. The best thing to do would be to look to other RPGs or games with RPG elements.
One possibility might be to introduce the long-debated "combination system," where breeding (or a Monster Rancher-type ceremony) can be used to DRASTICALLY alter the stats of your Pokemon by taking an aspect of one Pokemon and combining it with another, instead of merely passing on natures, IVs and moves. Such a system would either expand the current breeding system or even run congruent with it, achieving somewhat similar results, with the focus shifting slightly from a long, arduous process and more towards a faster, more practical system. However, like with Monster Rancher, the presence of "Luck" in the process would undoubtedly keep it from becoming too surefire.
Returning back to the 3D aspect for a bit, perhaps a greater emphasis on the Battlefield will change how we plot our strategy? Attacks like Earthquake, Surf, Lava Plume or even Explosion could alter how some Pokemon interact with the battlefield, possibly adding offensive and defensive options for both battlers. Perhaps now, like in a tactical RPG, it would become even more important to think ahead a few turns before you make your move, as a move's AFTEREFFECT could directly affect your opponent's next turn AND your own! Imagine this:
You are fighting on an arid grassland. You are using Ninetales, and your opponent is using Vileplume. You COULD go for the kill directly with Flamethrower, but doing so will ignite the surrounding landscape, making it dangerous for you to switch in your Pinsir later on!
Such a change would open up a whole new sense of team synergy. Now it would become important not only to pick Pokemon that work together based on typing and role, but also on the types of moves they use as well. Whole strategies could be plotted on keeping certain "field effects" rolling throughout the battle... and old field effects like Gravity or Rain Dance wouldn't become obsolete. Instead, they could be enhanced or even countered by certain other kinds of field effects. Such a change would force a much, MUCH greater emphasis on team strategy instead of filling roles or boosting a generic sweeper.
