As an owner of a 990R and a 690R it would be a very tough decision choosing which one to part with if I could only have one. Hopefully that day will never come.
They are both so different from one another, but as you spend time on each one you realize the subtle similarities. You'd see what I mean if you rode them both for a bit more time than a short test ride. The suspension on each of them is pretty hard to beat for a stock bike. And when you pin the throttle the fun factor shoots to 10+ on each of them.
My only advice is test ride both. Then think about the real purpose for the bike,,,, more trail duty or more of a 50/50 ratio dirt to asphalt.
I personally find the 690 a much more enjoyable bike off pavement and the 990 a great 50/50 machine.
2012 KTM 690 R
2012 KTM 990R Adventure
2014 BMW GSAW
"Walking thru life to an unknown destination and trying to enjoy the adventure getting there"