KTM vs. Yamaha: yup, they feel different. Which is better depends on what you're used to. I personally like the KTM and feel very much a part of the bike, but hey different strokes.
On parts prices I find them to vary dramatically. Some are easily explainable, like hydraulic clutch parts are more expensive than cable parts. On the other hand why are KTM plastic panels half the price of Japanese stuff? Magazine comparisons usually show KTM parts midpack overall in prices, but with wild swings from part to part. YRMV.
On parts availability, part of it could be the dealer, but KTM put lots of money into inventory over the past couple of years. I get stuff very quickly, quicker than from Honda (previous bike).
Good luck!