I doubt that extending Route 3 at all is politically feasible even if the technical side worked out. From a technical standpoint, the issue with truncating the road wasn't that cars couldn't go through, it was that they couldn't go through to Boston. Unless a significant amount of the traffic at that interchange is headed to East Lexington and Arlington, adding a direct feed to Middlesex Turnpike won't help much. The traffic will still pile on the tiny loop ramps and the new mainline will be empty.
A cloverleaf is better than what's there, but it's not great for flow either. What's needed at Route 3 is the same kind of interchange MassDOT has planned for Canton:
http://www.mhd.state.ma.us/cantoninterchange/images/ENF_alt.jpg
The key is the high speeds and large curve radii, with multiple lanes from the terminating road to both 128 directions. Of course, there's more going on in Burlington, and any new interchange will likely need to accommodate a new Middlesex Turnpike setup and perhaps a new ramp directly from 3 to MT.