The major difference I've noticed is speed and stability.

WM6 lagged quite a bit once I got it all my third party apps installed and tweaked the way I liked. I also use Pocket Hack Master to overclock the processor, and it would not be stable at anything above 400MHz.

WM6.1 runs fine at 450MHz, which provides a noticeable jump in speed, which in turn makes running all those third party apps much more enjoyable.