I had an '08 550 and raced it in Vegas to Reno in 2011. As a tribute to how amazing the bike is, we ended up 8th overall that year! I also competed in that race in '06 and '07 on an XR650R and, hands down, the Husaberg was FAR superior! Makes me wonder how on Earth Honda was able to win so many Baja races on that pig. The Husaberg was superior in every way. It handled better, weighed less, made more power where it counted (the Honda has better bottom end but, really, that's the only place it outshined the Husaberg), and required less maintenance. On this last point - in '06, we had to change the air filter 3 times on the Honda. In '11, we finished the race on the same filter we started with.
How the 550 compares to the 650, I can't say as I've never ridden a 650. I have, however, finally gotten my 660 running and, for what it's worth, will say the following. My main goal when building the 660 was to have an engine with the same character as the 550 but with more power everywhere. My 660 is a highly modified early 600 engine that's been bored to fit a 100mm piston and I believe that I've achieved my goal. There's nowhere that this engine doesn't make power and I recall thinking the same about the 550.
As far as reliability goes, my 550 never missed a beat in the 50 hours that I put on it before selling (which I deeply regret but the money to remodel the bathroom at home had to come from somewhere). My brother has an '06 550 with closer to 100 hours on it and it has also not missed a beat.
Also, I no longer consider it a deal-breaker when replacement rods are unavailable. I had a custom Carillo made for my 660 and, although it was expensive, it's rebuildable and quite beefy. I doubt that I'll ever have a problem with it.
I'm sure you won't regret buying a 550. As a matter of fact, I feel that those '05 models were some of the best looking 'Bergs ever produced.