I want to provide a little history, and a little rant.
Charlesgate Park was designed as the Beacon Entrance to the Back Bay Fens, one of six grand entrances.* Like the Fens itself, it was mostly wild - it was not intended as a formal park like the Common. Instead, it was for sanitary purposes: the tides would wash the basin twice daily, clearing out the outflow from the Muddy River and Stony Brook, which were used as sewers and which tended to overflow during storms. The plants were picked to withstand the saltwater. (After the Charles River Dam was constructed in 1910, the Fens and Charlesgate were freshwater, and parts of the Fens were filled in for recreation.)
Nonetheless, it was a pedestrian-friendly area. There were paths along the edges, with elegant hotels opposite. There was a graceful crescent-shaped bridge over Ipswich Street and the tracks. Its sidewalks led directly to the Commonwealth Avenue Mall, which was continuous all the way to the Public Garden. Two low arches were added for Commonwealth Avenue in the 1910s, replacing an older span. Once you crossed narrow Back Street, you were in the Esplanade, where a footbridge crossed the mouth of the Muddy River. Charlesgate was indeed a gate - the string that connected two of the Emerald Necklace's pearls, plus the Esplanade.
This was stolen from us in the name of traffic. The Mass Ave underpass severed the Comm Ave Mall. Today, you can't legally access the median of Comm Ave between Charlesgate East and West - which means you can't even cross Comm Ave without leaving the park. (The lovely Mall between Charlesgate and Kenmore is now practically abandoned because it's no longer on a through route to the other parks.) Storrow cut off the park from the Esplanade. The Pike took the curved bridge. Bowker stole the sunlight, fresh air, and river, and cut it off from the Fens. This wasn't a single bad decision - it was a half century of decisions to take away a beautiful space so that suburbanites could have their cake and eat it too.
The NEU plan is a good start - it's a recognition that this indeed a public space that should be treated as such, and that it is a hub that connects other green spaces together. But ultimately, we have to confront the fact that the mere existence of the Bowker Overpass is a bad thing, that it needs to be removed, and that almost every vehicle that uses the Bowker is the result of a policy failure. Every nurse that drives from Chelsea to the LMA, every NEU employee that drives from Waltham, every Back Bay resident that drives to their office off 495 - there are distinct and reversible policy failures that led to them choosing to drive (or having to drive), and for their route taking them on roads that cut Boston off from its green spaces.