I work closely with the Muddy. The daylighting of the Muddy in front of the Landmark Center was the first phase of a wider, multi-phase environmental restoration project for the Muddy River. This wider restoration project is a joint effort between Boston, Brookline, the state, and the Army Corps of Engineers.
http://www.muddyrivermmoc.org/
The next phase will remove the vast majority of the invasive reeds and plants in the Fens and Riverway, dredge significant portions of the river from the Fenway up to Leverett Pond, and replant/regrade the landscape in line with Olmsted's original plans for the area. This second phase is currently out to bid for subcontractors, and, with any luck, will be starting next year...
...as for the river's slow flow, the Muddy's change in elevation from Wards' Pond in Olmsted Park to its "mouth" at Charlesgate is literally a foot. There's never going to be a lot of flow, so it's imperative to keep the River maintained more than it's been in the past.
A small write-up:
https://thebostonsun.com/2018/10/26/parks-department-proposes-phase-2-of-muddy-river-project-blc-denies-flood-wall/