http://img843.imageshack.us/img843/5189/pikei.jpg
Here's my very crude rendering of what I think the Allston tolls could look like with a realigned Pike, taken from a Bing Maps birds-eye screenshot. Went with a compact ramp design to maximize the amount of redevelopable land. South (BU) is up, north (Harvard) is down, east (Back Bay) is left, west (Allston) is right). That's a ramp-less Cambridge St. front and center. The Pike west to Storrow east ramp inclines down from elevated to at-grade where it merges with the (at-grade) Pike east to Storrow east ramp. The Pike east to Soldiers Field west ramp inclines up to merge with the elevated Pike west to Soldiers Field West ramp. Other than that, the should be fairly easy to see what elevated and what isn't by the overpasses/underpasses.
Blue arrows = Soldiers Field Rd. west traffic flow (or combo exit ramps).
Green arrows = Storrow Dr. east traffic flow.
Yellow arrows = Mass Pike east traffic flow (or combo entrance ramps).
Orange arrows = Mass Pike west traffic flow.
Red shade = redevelopable land.
Green shade = parkland.
Rust shade = highway/undevelopable land.
High-speed tolls with the overhead transponders moved back a little further towards Cambridge St. Space for 1-2 manual booths in the right lanes, but otherwise they're speed-limit tolls.
New configuration re-uses a small half-width (2 abutments) portion of the viaduct for the new westbound exit ramp, and a portion of the existing eastbound entrance ramp onto the viaduct over the current toll plaza is retained for the new eastbound onramp right after it splits from the westbound onramp. The new Storrow east onramp is superimposed directly on top of the Beacon Park U-turn lane. New ramp construction on the Soldiers Field flyover, the new flyovers of the relocated highway, and the sections of the Pike east entrance on either side of that recycled bridge. Nearly all else is at-grade. 3 totally demolished bridges, and over a third of the viaduct gets demolished. Cambridge St. bridge over the lone remaining ramp can get shortened to half its current length and filled in.
Lotsa land recovery, no? Note...doesn't include any ramp possibilities west of there. There's absolutely room to put some ramps to Brighton. I drew it so there'd be about 4-5 tracks of buffer still left on the Worcester Line for peeling off another ramp upstream or plunking a commuter rail station under the Cambridge St. overpass.