@ Chris, I find it hard to believe you don't here any improvement after upgrading to firmware 4.10, as many users above and myself, really did notice the difference in MT qualiy (less jitter). Don't get me wrong: I'm not saying it's perfect and as far as I can recall, my (sold) pair of CDJ-1000 MK3's performed better on MT.
At least for me, since 4.10 I can again use the MT function for beatmixing with the CDJ-900, although I rarely speed a track down or up by more than 5%. And yes, I think Pioneer should further improve the MT on the CDJ-900/2000.