I was thinking, it would be a lot of fun to do coop runs with my friends. For example, we both start a new character or start anew in a zone, and we go through the content together. Since we are linked, we are in coop mode, which basically means we can each fight our own NPC at the same time, but when my friend beat his NPC, it will also be beaten for me. The first Poke in my list will get the same XP my friend got, which is needed because I'm effectively skipping half the trainers which would mean I would level too slow for the content.
When we reach NPC's that are strong (gym leaders) we can decide to team up against them, using only our first 3 pokes each.
If my friend hasn't played for a couple of days and I kept leveling, I can still team up with him, but now only I talk to all NPC's so I'm basically power leveling him to reach my level again. This is more fun for him because now he can still keep his original pokes, instead of me just giving him higher level pokes.
I think this could give a new dimension to the way PokeMMO is played, at least for me it would.