I had an '01 F650GSA for about 3 mo. / 2,500 miles and really LOVED it!! The only reason I sold it was to get my 1150GS back (long story). Funny thing is that I miss the Baby GS much more than the big pig.
The BMW dealer flashed the latest FI map for about $30 to fix some random stalling; other than that it was all trouble-free miles. Maintenence is much more involved than the BMW boxers, but if you usually pay for service then it is no big deal.
I'd buy another one in an instant if I had the $$
One thing though, if you plan to get on some trails with it, I'd go for the higher Dakar.