I posted a Hub with all the reasons I can think of but I will briefly explain my reasons.
1. Can not be made for PC due to Exlcusive rights for the Pokemon franchise.
2. Would be made for Wii U, would not be made for the hand helds like normal.
3. How would they profit for it, since servers cost money.
4. Would time be better spent making games like pokemon conquest, pokemon ranger, and the main series of Pokemon? Could we justify spending all that time on an MMO and make it work?
5. How many gym leaders would there be? and would there be more then one Pokemon Elite four?
Those are just some of the reasons why they have not made a pokemon MMO. There would be a good chance for it to not be worth it in the end.