The 627cc motor in the 650 was the "last" of the SOHC4's and has the best of them all. It has a true hemispherical combustion chamber with slightly domed pistons. The camshafts are basically the same, though the 650 has a tad more lift and slightly more duration. If you put a really hot cam for the 550 into a 650, you won't be as "extreme" though you've got the extra cc's to make up for it. The electronic ignition is great, I haven't had any trouble with mine thus far. The charging system can be a pain, though if yours works and you go through the connections to eliminate corrosion you shouldn't have any trouble.
About putting a 650 motor into a 550... I'm not sure about the balancing of the frame, etc. but there are more aftermarket parts specifically for the 550, so that could be the advantage of the 550 frame with the 650 motor. Also, it kind of makes it more of a "sleeper" if your race buddy doesn't really know what he's looking at. "I can whop a puny 550..."
I've got a '79 650 and I replaced the mains, went from 90's to 102.5's. Removed the stock aribox cover, and will be slightly drilling out the exhaust. After just the jet change and cover removal, all I can say is, "WOW!" It'll lift up the front tire in 1st and 2nd. I've never ridden a 550, but I don't think many of them are doing wheelies...