I think it's too early to develop an MMO. The technology is there, but few MMOs have been released in consoles (let's see how FFXIV will do). I think Pokémon needs a revolution in the battle system, which is too simple (maybe there's why people like it, but...), in a way similar when Effort first came in Ruby & Sapphire.
In fact, I think this training system needs new features too. Although I think it's a great mark on the series, Effort Training is too repetitive and maybe that's why people end up by using Pokésav and alikes.
Exploration could be different, too. I've always though of exploring gigantic cities by unlocking "areas", which would be selected at the entrance. Sounds interesting for me.
To keep the series at least changing a bit in a while, I don't mind new moves or abilites, I just don't want ANY new Pokémon created: Zoroark really resembles a Telefang monster (or, as we, know in the West, Pokémon Diamond & Jade).