I like both bikes for their own reasons, but if I had to choose I'd go with the 550, especially if the 650 you're looking at is already having charging system problems. It may be a simple fix, but it could also end up being a huge headache you are forced to deal with before you can ride your bike. Of course, the same could be said for pretty much any old vehicle.
Power difference is negligible. Thee 550 ride is a little more sporty, where the 650 is more of a mild cruiser with a lower-slung seat and leading front axle. The 550 carbs are easier to work on and make adjustments to. There are benefits to the CV carbs, but I just prefer the old style carbs for their simplicity. The 550 has a kick-start, 650 doesn't. If you like that the 650 has a points-less ignition, a dyna-s can be installed in the 550 for $125, as well as some more and less expensive options. The 550 can be easily hopped up by installing a stock 650 cam and making a slight change to the drive sprocket/s.
Like I said, I like both bikes and would be proud to have a 650 in my garage, but the 550 is my preference.