Emily and Morgan have a natural tension because they're both alpha personalities. They're both the types who could pick up a stranger in a bar and brag about it the next day, they're both the types who can walk into a room and naturally have people's attention. They're not afraid to speak their minds, they're both very empathic, but still though and I can imagine both of them leading in a drinking game, poker, whatever.
This kind of "clinch" of personalities, in my opinion, happens more when the persons are somewhat similiar - equals. The chemistry Morgan and Garcia have is on a different level, because they're very different as persons. This kind of chemistry is more like the one Morgan had with Todd, although he and Todd were more like two siblings constantly fighting. He had a similiar relationship with Elle too, from season 1/2, but she was more "angry" than Prentiss is, so I think he felt more protective of her, or, well, was more aware of her weaknesses and how prone she was to them. I think he trusts Prentiss more than some of the others in a bad situation, because he knows she would react the same way as him.
This is, IMO, the reason for the tension between them. Sometimes I think they should just get it on and get it over with, but at the same time - maybe they're TOO similiar. If they were to be a couple, they'd be one of those couples always making crude jokes at each other, always being competetive in activies and sports, they'd be more like two great friends in public. I don't know, what I like about this show is that everyone doesn't hook up all the time. That they can just respect each other professionally and be great friends and feel like a family - no sex involved.