right now MechJeb refuses to use the new abilities of the SAS and handles the craft itself, but this results in bumpy and wobbly movements like back in 0.20
Can you please fix this

No that's for now NOT fixable because currently SAS would override MJ and not allow it to change the controls.
It might be possible with changing how MJ changes them but that's something no one (afaik) has looked into yet.

r4m0n added a "Use stock SAS" option in Attitude Adjustment in 2.1 for those who want to test it.