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they're two completely different speaker sets. If you're just worried about the additional speaker, it mostly depends on your physical arrangement. If you can sit in the sweet spot - directly between the front speakers and (I think, correct me if I'm wrong, knowledgeable guys?) twice as far away as the distance between the speakers - a center channel really isn't that much use. The center channel, as I understand it, is mostly there for situations where some of the people listening are not in the sweet spot, so dialogue will still appear to be coming from the TV and not from three feet to the side of it.
I just made that exact change/upgrade. I am an audiophile as well as a gamer. I made the change because I wanted to upgrade my wife's setup, too, and her speakers were old and cheapo. As you know, the 560s are a mighty good set of speakers in their own right.
After a couple days listening, and a lot of tweaking, I am getting used to the 5500s. I was not blown away as I expected to be. Two reasons: as I said, the 560s are pretty good already, and second, the bass is louder perhaps, but not as precise, so they will sound "different" at first. They definitely rattle the walls. I would say go for it for another reason, though and that is you can better access true 5.1 sound with the 5500s as opposed to 4 channel quadraphonic. You did not say whether you watch movies or not... if yes, then upgrade.
Also, what sound card are you using? You might get a better bang for the buck by upgrading to a high-end card if you're using mobo sound.
In the end, no question BF:2 sounds better... but it still is an average sounding game. A better example is HL2--it is amazing. I hear F.E.A.R. is awesome too, so you might want to check that out. Good luck!