Parra,
I had a '05 1200 GS, rode it two years and put 45 000km on the clock. Great bike! Loved to ride it, even took the bike to Daytona to play.
Then I sold the bike April 07 and bought a 2nd hand '05 950 Adv S.
My reason for the change - I prefer the more off-road capabilities of the KTM, plus the look draw me. But then again, I never reached the 1200GS's limits off-road. I knew the bikes limits and rode around it. With the 950 I don't worry as much about ground clearance, final drive taking strain, etc.
I do however worry about dinging the front rim (which can be sorted with an after market rim).
For me the two bikes are in many ways similar, but in other ways so different you cannot compare them.
Do I regret my decision? NO! The KTM is more suited to my riding preference, and I still enjoy getting on it, even after two years and 34 000km.
For me, the KTM can do anything the 1200GS can, somethings way better, some on par and some below par. The BM cannot do everything the KTM can.
And reliability.... just check all the 2007 BMW 1200 GS/A recalls... you get "duds" in all brands. A good brand will sort the problems out and deliver a good quality product.
Lastly, both brands have a 2 year warranty (KTM - no "On Call" facility); the std 990 Adv comes with ABS.
So, to summarise. It is all about personal preference.