I'm no suspension expert but I have ridden a poorly suspended KLR. I did work real hard to improve that KLR suspension but these bikes are all so much better. I was lucky to find bikes that had great suspension upgrades.
The 640 came with the SPS suspension and has worked great. Its had the most use off road; Death Valley and the Pony Express Trail across NV.
The 990 came with Precision Concepts suspension and its worked great the last couple thousand miles of mostly road.
Both PO's of the 640 and 990 had set the suspension up close enough to my weight. If I had to have work done on these I'd go to SPS, it is so close and James does excellent work.
The 400 came with Trail Tricks but set up for a much lighter rider. I stopped by Javier's shop on my way home from buying the bike and had it tuned for my weight. I was the only one at the shop that morning and Javier's tech did a excellent job. Unfortunately I have not had a chance to ride the 400 on trails yet. Thats the part that sucks.
2010 KTM 690 Enduro R
2006 KTM 950 Adventure S
2002 KTM 400/453 EXC