I've owned two KTM950's (but not a 990) and both a R1100GS and a R1150GS Adventure. And am now a new owner of a 2013 R1200GS Adventure for just a few weeks and a few hundred miles. So, I do have 50K+ miles experience on the KTM950's and 150K+ miles on oilhead BMW's.
When I came to select a new adventure bike I considered both the KTM990 and the R1200GS Adventure. I selected the BMW despite the fact that is cost a lot more money. Reasons: Primarily I did it as I wanted one of the last air/oil cooled boxer motors before they do to the water cooled models this summer. Secondarily, both the PITA (pain in the ass) of the maintenance of the KTM bothered me as it was a royal pain to do a valve adjustment, etc.. and the fact that, IMHO, the KTM950 lacks the torque that the BMW has. Meaning, the KTM was a hell of a lot of fun but I felt like I had to row the gearbox a LOT to keep it in the power band where I wanted it. I live in Colorado so we have less power up here.
I think the fact that the BMW has more torque, or at least it feels like it does, works better for me. When I'm out touring around or playing with the sport bikes I am not shifting all day. That was very appealing. The 2013 GS Adventure to me is a lot of fun and does very well in the twisties but it is not going to feel like the KTM and vice versa. If I was going for a long journey (1000+ miles) I'd pick the BMW every single time over the KTM.
The bike doesn't feel lame to me. It runs just fine right out of the box and the stock exhaust has a nice snarl to it compared to the R1100GS and R1150GS Adventure bikes which DID sound like sewing machines. I think BMW has made a lot of good progress with the latest GS.
Just my .02.