The Stars of the Show
We've covered how the worlds will work, but have yet to touch on the actual monsters that this game revolves around. The most important thing this time around is that all of the Pokémon will be unique. Not just in terms of character design, but in terms of actual usefulness. One of the biggest problems with the Pokémon franchise right now, from my point of view at least, is a lack of variety. Pokémon are designed in every which way, but they all pull moves from the same general pool. You could have a dozen fire Pokémon, but odds are that they'll end up learning (or being taught) the same general moves. The only reason to have multiple fire Pokémon, in most circumstances, is because they have different stats. Pokémon are effectively bundles of stats, which you end up teaching the same general powerful moves at high levels. You end up trying to "catch 'em all" solely for the sake of completion, not because you want to exploit some particular ability that a Pokémon has.
With such a huge number of Pokémon, though, it would be exceedingly difficult to create a set of unique moves for every single monster. There's nothing I'd like more than 400 Pokémon with completely individual moves, but I'm fully aware how unlikely that will be. One solution would be to drastically cut the number of Pokémon, maybe even down to the original 151. I will admit, however, that I like the fact that there are a lot of them. It gives the impression of a more diverse world, and I like the whole "catch 'em all" idea. I think a better idea would be to radically alter the method by which Pokémon learn moves, and battle in general.
If you catch a Pokémon in the wild (a relatively low-level one), it won't know any moves. That is, it won't know any of the typical TP-consuming type of moves that are the current standard in the Pokémon games. Many Pokémon are just squirrels and birds, things of that nature. They aren't natural fighting machines. As such, they start out exactly like what they are - wild animals. All they'll be able to do is scratch with their claws, peck with their beaks, etc. The most notable thing about all this, though, is the nature in which battles would be fought.
Imagine two CPU characters fighting each other in Super Smash Bros Melee. Or Tales of Symphonia with all characters on auto, and all techs disabled. Basically, you've got two opponents battling it out without any user-input, dependent solely on their inherent AI fighting routines. This would be the most basic form of battle in this new Pokémon game. You can't expect a monster that you just captured to be a fighting genius. If you suddenly release it from a Pokéball, it will fight wildly against its opponent based solely upon instinct. From a technical standpoint, this is its default AI routine. All Pokémon, when pitted against each other, will fight based upon an AI that you help cultivate throughout the course of the game.
So how do you develop this AI? Any activity that you involve a particular Pokémon in will help mold the way it acts. Let's say the Pokémon is a grass type, and you routinely use it against fire types. As any good Pokémaniac knows, grass gets owned by fire. So after being continually beaten up by fiery foes, your grass type starts acting more defensive when battling against those types. Perhaps it even develops a complex, and refuses to come out of its Pokéball when you try and pit it against a fire type. In this fashion, your Pokémon will learn to trust or distrust you. Giving potions when your Pokémon is hurt, pulling it out of battles before it faints, these are all things that will cause your Pokémon to trust you more. And if it trusts you more, it will likely behave better in battle. It will be generally braver and more responsive, knowing that its trainer is there to help it out.
Outside of fighting battles, there will be numerous other ways in which you can train your Pokémon. Let's say your Pokémon's main weakness is its speed. You can take it out of its Pokéball in a field, and run around with it. It will slowly but surely become faster as you train it in that fashion. If it's weak, you can have it carry around something heavy for a while. It would be very similar to training your creature in the PC game, Black & White. You would have to be careful not to over-train your Pokémon in a single stretch of time, however. Too much training and they'll faint, preventing any further training for a good chunk of time and lowering their trust of you. It would be a necessity to prevent players from making their Pokémon incredibly strong in a very short period of time.
Then we have special moves. They would work similarly to the special moves in the current generation of Pokémon games, consuming TP with each usage and having a particular offensive or defensive effect. The method of learning special moves would be slightly different from the current games, however. For instance, you could have your Pokémon learn a different initial special move depending upon the style in which it has been fighting the most. If it's been particularly offensive, it might learn a new attack. If it's been getting its butt kicked, it might learn a new defensive technique. Depending upon the initial move your Pokémon learns, it can then proceed down a particular series of learnable moves that are related to the original move. Use the original move 50 times and your Pokémon will learn a more powerful version of the same technique. It would be very similar to the method of learning new techniques employed in Tales of Symphonia. A Pokémon's proficiency at performing a particular move would also improve as it uses a move more and more. A Pikachu that has just learned Thunder Shock may miss often, and be lacking in power. A more experienced Pikachu would have a considerably more accurate shot, and likely do more damage with each strike.
Battles themselves would take place in a 3D area filmed from a primarily isometric camera angle. Each trainer would stand at opposite ends of the screen as their Pokémon battle in the middle. Things would play out like they do in the Pokémon cartoon, with the two monsters running around and fighting against each other freely. Your most basic job as a trainer would be to assist your Pokémon's standard AI with vocal commands. If the enemy is sneaking up behind your Pokémon, yell "watch out!" to try and warn it. If you see a weakness in the enemy's defense, order your Pokémon to quickly strike. Much like the ATB (Active Time Battle) system used in the PSX era Final Fantasy games, each Pokémon would have a time bar that denotes when they can use a special move. The speed at which the bar fills up would depend upon that Pokémon's natural speed, and while the bar fills up the Pokémon would run around and fight with its natural abilities. Once the bar is full, the trainer decides when and how the special move is to be used. You can immediately call out to your Pokémon and order it to perform a technique, or wait with a full bar and have your Pokémon perform the move with particular timing based upon how the battle is playing out.
Performance in a battle would depend upon how well your Pokémon was trained, and how well you worked with it during the fight. If you did a lousy job with training and just tell your Pokémon to use techniques over and over again during a fight, a more battle-weathered Pokémon might be able to easily evade your attacks and even adapt to some of your techniques. If you don't time your special attacks well, the opponent's Pokémon may block or evade the move. The best trainers will spend individual time with their Pokémon to strengthen their stats and base abilities, and battle with them often to refine their strategies and general battle-readiness. There could be a multitude of ways in which you could train for specific circumstances, perhaps even by pitting your own Pokémon against each other and training them to adapt to certain attacks or techniques.
Concluding a fight would involve more than merely depleting your opponent's HP. Perhaps, similarly to the Super Smash Bros. series, Pokémon could accumulate damage infinitely, and that damage increases the odds of them fainting. Actual fainting would depend upon a myriad of hidden statistics. Was your Pokémon exhausted from training or previous fights? Due to a low level of friendship, does it simply not have the will to continue on after sustaining a lot of damage? Could it keep fighting much longer than expected due to having some kind of personal stake in the battle? How many times have we seen Pokémon in the cartoon win or loose battles for these very reasons?
The whole idea here is that you aren't just some guy who captures various monsters and forces them to fight each other. You legitimately take the role of a Pokémon trainer, and work with your team to win battles and become stronger. If you just sit back and watch your Pokémon fight, you'll find yourself quickly bested by trainers and Pokémon that work as a team.