Red Line only gets real deep around Porter and Davis, and that was done mostly for the benefit of the Porter-to-Davis stretch where the line deviates from the street grid and starts going underneath people's property. It eases back closer to the surface for the Davis-to-Alewife stretch where it mostly snakes underneath the old surface freight line (now a bike path). That ROW has no additional surface grade crossings once it crosses Mass Ave., so it would've been feasible to do simple cut-and-cover for the last leg with minimal surface disruption...especially since there weren't nearly as many residences abutting the old freight line back in the early-80's. Whether or not that's what they actually did 25 years ago, I don't know...but the existing ROW probably had something to do with how deep they went. Once it reaches Alewife the depth is back to about 1 story below ground...and I think the tunnel stays that depth until it ends underneath the Minuteman Bikeway on the other side of Route 2 (right around midfield of the soccer field in that park, if the location of the last emergency exit is any indication). I imagine if they opted to extend the line into Arlington they could've done it cut-and-cover most of the way below the Minuteman, except for maybe Arlington Center when they'd have to go under the big Mass. Ave/Route 60 intersection.
Old-construction RL tunnels are fairly uniform in depth. The Harvard-to-Longfellow tunnel stays 1 story below street level the whole way (sunlight even reaches into the tunnel late-afternoon via the emergency exit on the inbound side right after the animated ad), and the Charles-to-Andrew segment stays 2 stories below street level due to the trolley tunnel/provision built immediately above. The tunnel portions of the Ashmont line are all simple cut-and-cover (and may not technically be below ground for parts of the way).
Green Line is cut-and-cover all the way, save for maybe the last stretches to the C- and D-line portals (they both go below the Mass Pike, and the Mass Pike is below street level at that point...therefore it's at least 2 stories below street level). Given the relatively high number of portals and former portals along the route (Comm. Ave., old Kenmore portal, Huntington Ave., Boylston St., Public Gardens, Tremont St., Haymarket, the "new" Science Park portal)...there's not really any chance along the way for the line to dip too far down.
Blue Line gets real deep just before it goes under the water, but it gets shallower in a hurry. By State it's at the same depth as the Green Line, which is why they had to remove the floor at Court Street in order to extend the line to the other side of the Tremont Street tunnel to Bowdoin and the old portal. And the Maverick end can't be too deep given proximity to the portal.
Orange is either cut-and-cover or just-plain-cut in the SW Corridor, though it gets pretty deep at New England Medical Center (probably to allow for extension above of the almost-adjacent abandoned end of the Tremont Street tunnel). Starting where the new tunnel hooks into the old Chinatown tunnel it's back to just below street level (Chinatown inbound is VERY close to the old portal), and that's where it pretty much stays save for the sudden and dramatic "dip" at State. The Haymarket-North tunnel also goes a little deeper into the bi-level new North Station...and then it feels like a long climb out to the Community College portal.