My experience is that 1.0.x has clearly and considerably worse performance with high part counts than 0.90. It's probably, but not definitely, down to the new thermal and perhaps aero system. The extended physics range is a factor too - in older versions once your dropped stages got 2.5 km away they vanished getting rid of the CPU load, now you still suffer that until they're over 20 km gone. 0.90 I still consider the best KSP version, the gizmos revolutionised VABwork and as a committed FAR user I have no interest in the newstock aero, though I know some Windows players had a lot more trouble with its stability than I have on Linux. 1.0 through 1.0.4 I consider the worst KSP versions since I bought the game, with their glacial performance and shoddy thermal system. I've yet to play 1.0.5 enough to really make a conclusion, though my preliminary results are that game performance hasn't improved over 1.0.4. If it wasn't for new FAR along with Kopernicus, I'd probably switch back to 0.90. Unfortunately the modders all swiftly move their efforts to the new KSP version whether or not it's actually any better than the one before.