The arguments for and against removal of this overpass are similar to the discussion that happened on here about removal of the Bowker overpass. Both cases seem to boil down to whether removal of the overpasses would create unacceptable traffic congestion. I always like to step back and think: what if these overpasses had never been built in the first place? Would they even be missed?
No.
Motorists would have operated in, and adjusted, to whatever traffic ecosystem was available. For example, there are no overpasses at the River Street and Western Ave crossings of Memorial Drive, which are certainly major intersections, yet they work okay. The junction of Routes 2 and 16 at Alewife is similar.
I like to posit the opposite question: What makes you think the absence of an over/underpass is preferable to having one?
Generally speaking an overpass is taking some significant percentage of the traffic volume and putting it somewhere where someone who is a pedestrian or cyclist doesn't have to deal with it at all, and is making the intersection they do have to interact with less complicated and have fewer lanes/movements. To me, that often outweighs the downside of their lack of beauty in terms of impacts on me when I am a pedestrian/cyclist.
If this state could somehow be less negligent with maintenance and actually keep them clean/painted, well-lit, and not dropping chunks of concrete and paint chips, I'd feel even more strongly that way.
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River + Western are one-way and don't need as many light phases, which helps them be a little bit less of a bottleneck than it looks like they should be at first glance. The light at the Anderson Bridge/JFK St is the only plain 4-way signalled intersection on Mem Dr I think.
The Alewife mess is basically saved by the surrounding segments of the Alewife Brook Pkwy being so broken that it manages to look "good" in comparison. It also has almost no interaction/conflicts with non-motorized users to worry about.
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Now, with all of that said: I'll also agree with the critique of their overpass concept.
I see absolutely no reason why you need an overpass that's 2 lanes in each direction. A roadway that only has two lanes at traffic light controlled intersections cannot move 2 full lanes worth of free-flowing traffic in each direction. Especially with left-turn movements existing at some of them.
So I'm entirely in agreement with previous mentions suggesting to rebuild the overpass but with only one lane each direction.
Should cause about zero change of actual vehicle throughput, moderate traffic calming on both the overpass + the roundabout (from being able to achieve more optimal entry/exit angles that force slower speeds), will let you reclaim as much as 20ft+ of cross-section in some spots, and will completely eliminate on-ramp merging (and the challenges people have with it + managing their attention).
The two combined will let you greatly improve safety + user-experience for non-motorized users, significantly more so than DCR's emergency fixes on the south side have.
