A few points I'd like to make, some more relevant than others.
I'll get you, Pokémon!
For example, in fire, in water, in grass, in forests
in earth, in clouds, in that girl's skirt (eek!)
-Mezase Pokémon Master (translated)
I'm not sure maintaining a turn-based system is necessary. Personally, I've long envisioned it sort of like the 3D Legend of Zelda games in terms of free movement. And while I'm a little averse to MP meters for a Pokemon game, something similar could (should?) probably be employed to make things more realistic. That would get past the artificial "you can't use more than five Fire Blasts!" limitation, which would be more suitable for getting people involved in the world.
As you said, not all Pokemon games these days rely on that counter, so why should an MMO of Pokemon? Decreasing the "energy loss" from using a powerful move could, in my view, be a valuable reward for levelling up.
No offense, but this seems a little overcomplicated to me. A few adjustments wouldn't be bad, but only to add to the realism of the world. Easy example regarding the "MP bar": it no longer wears me out to throw ten consecutive roundhouse kicks, but it was a little tiring when I started martial arts. In contrast, it's impossible to throw a double roundhouse until you can do a single roundhouse, and the advanced double jumping snap kick must be preceded by learning a single snap kick.
It would make a little more sense if, say, a Pikachu could learn Slash before Thundershock; just as some people learn certain kicks before punches, a Pikachu might learn claw strikes before honing its electric powers. But I think you'd have to be very careful to avoid overcomplicating matters; at most, maybe you'd have separate stats for Physical and Special moves.
The question still remains how you'd accumulate Exp. points for each one individually. Would the game keep track of the moves you used of that type, or something? What about Pokemon who only know one type of move but might learn the other later... how would one accumulate Special Exp., for instance, if it knew only Physical moves?
Totally agree with packs to unlock new lands. Not so sure about influencing NPC's Pokemon, but maybe there would be sufficient appeal in, say, dodging Zubat.
Does the Wii have the proper capabilities to handle an MMO? People have had enough trouble with Super Smash Bros. Brawl battling; I worry about what might happen if dozens, even hundreds of trainers were in close proximity with one another in one location. When the movements of three human players are significantly delayed, what would happen with an MMO? This is one of the central obstacles for this project... the developers would almost certainly have to make use of computer hardware rather than that of a Nintendo product.4)
... All that aside... It should be a 3rd Game for the Wii, IMO. And in any case, more cut scenes are needed. The game, and anime, suffers from static dialogue at some points: too much text (and "!" signs), and too little action (including sudden changes in scenery and unexpected yet unavoidable sidequests).