I own a Fusion 550, 700RB-II, 2001RB, MB500 and MB200 (hoping to add an MB Fusion to the collection shortly!). As you can tell, I have become quite addicted to GK!
Though I have not played the 1001RB-II, if I may extrapolate from the 700RB-II (and a bit from the 2001RB), by comparison, the Fusion 550 has more harmonic content, which makes the high end seem a bit more bright, clear and exciting. You can cop some of this via the 1001's Presence control, though. The low end on the Fusion 550 is also a bit bigger and more round, though the RB's have more going on in the midrange.
I have not had any problems with the motorized knobs on the Fusion 550, though I do wish that the head would either mute the output (or else turn the Output all the way down, and then ramp back up) when you switch channels.
I'd say it boils down to how you feel about the harmonic content which the tubes provide, and how you feel about the tone profile of the Fusion 550 (bigger lows, somewhat scooped mids, more exciting highs) relative to the 1001RB-II.
FWIW, you can read my Quick Look review of the Fusion 550 in
issue #2, and Vic Serbe and Tom Lees' full review in
issue #3.
Tom.