Well, here goes.
One of the biggest annoyances for me is the load point bug. You can be in any bank, hold load to prime up a new sequence, and it will often go to a different bank, so you have to then switch banks.
The behavior should be at first load within your originating bank and if you want to change banks you can.
Something else I noticed that may be just related to my instruments but not sure: it seems like the pitch track you can assign to the aux CV out is an octave off from the regular pitch track. In other words, C4 on the aux pitch track seems to be C5 on the regular pitch track. Edit: I wanted to just confirm this - it is in fact my outboard gear which causes the problem.
As far as features I really really love to see: Foremost is an ext controller based step-recorder mode. So I can use my midi keyboard to record a step without being in live play-recording mode. It's really difficult to record a sequence with a midi keyboard on the MB2s. I think this is a very sore point. A step based recording feature would be very powerful. In other words, set it into step-record mode, press a key or a skip step signal and it proceeds to the next step to wait for your next input.
Another feature that would make this even more powerful is being able to assign the aux midi-cv outputs to a different channel so you can use them for independent midi in or out.
I'm sure there's more but hopefully this starts a little spark. The MB2S is already powerful but I think these simple changes could take it to the next level.