In this context, we're only discussing off-road capabilities. Long distances of slab may make you think otherwise - and to that extent I have zero knowledge of the Yamaha's road capabilities.
So in the context of which of the two KTM 990s for off road use, I'd say if you can find an R go for that one. The non-R comes with ABS. I have one with ABS and in hind-sight I really wish I'd have gone the other route with the taller suspention and more storage capacity under the seat without the ABS. Off road the ABS must be turned off. When I get back on the road, I rarely bother to go through the ritual to turn the ABS back on.
That's my $0.02
2010 KTM 990 Adventure
2010 KTM 450 EXC