The Mk3 is slightly less capable in the hover due to the higher wetted area caused by the big tanks and the slightly increased AUM. The Mk3, of course, came with the fittings for a probe, modified fuel system, fuel dump and IFR lights etc. Much, but not all, of this kit has been removed during the Mk3 Reversion programme. It is, however, IMHO a more stable hover platform.
The Mk3s also originally left Ridley Park with an analogue cockpit before flying to Louisiana for the glass cockpit. Now they are back in an analogue configuration they'll have all had 3 cockpits by 100hrs with a 4th to come....
Handling qualities? Hmm.....