I have all of them. They're not rare or expensive so you really can't lose. I think EX+@ had some exclusive characters than didn't show up on EX2+ or EX3. I know Akuma is one of them; can't remember who else was exclusive. I also liked the music in EX+@ better than the other two.
EX2+ had that bonus stage where you have to destroy a space satellite. That was interesting.
Also is it just me, or does EX3 have really crappy character art?