Yeah heaps of trouble. Bad news, next version probably won't be multiplayer compatible, I did everything I could but tModloader itself currently doesn't support everything needed. The only solution was to jump on GitHub and modify actual tModloader itself with more moddable net code. All well and good but that will take a lot more testing and then integration by bluemagic123 to become part of the main branch for everybody - but it did work.
As far as becoming NPC's they all are, and working, but making their AI more intelligent is hard and slow work. Before I was borrowing vanilla AI, but that isn't possible when they are no longer projectiles, and are npcs that can be turned on or off as friendlies or enemies.
So now I've got a rudimentary AI in place, for running, flying and swimming Pokemon but I feel like it's just not ready to go live, needs a bit more polish - and some more Pokemon. Every version needs a couple of new Pokemon to catch, that's a promise I made myself.
(For example I just made it so running Pokemon can jump gaps instead of just walking straight off cliffs in to a pit, Yay! But little things like they can't navigate slopes needs work)
I will be a bit busy with some important life stuff I have a deadline for, but rest assurred I am still working on it