Responding to the various points above.
One, the Charles River does have direct transit connections. The subway portion of North Station is only a few blocks from the eastern terminus of the Esplanade, and also is directly adjacent to Causeway Street where one can look out over the portal of the Thomas O'Neil Tunnel and across the Zakim Bridge. Alternatively, if Science Park station has reopened by the time this goes forward, that provides a more direct connection to the Esplanade.
Additionally, Charles/MGH station on the Red Line is directly underneath/connected to the southern approach of the Longfellow Bridge, which provides access to both the northern and southern Esplanade Trails.
Finally, the Boston University (historically Cottage Farm) Bridge is accessible via the B Branch of the Green Line, via either BU Central or BU West.
My intent for Storrow Drive/Soldiers Field Road was to walk the at least a portion of the section of the Esplanade Trail that parallels it, not ride on it via a bus (which I know can't use the road).
Mattapan has definitely been cleaned up somewhat, and is fine as long as you go in the middle of the day and stay on the main roads (don't wander into any of the back alleyways along some of the historic rowhouses). The situation of the stubs only being accessible via an industrial parking lot and a walk through the woods is why I considered them to be potentially inaccessible - if anything is going to be sketchy, it's going to be an industrial plant that is out of service on a weekend.
In terms of service frequency, I had no intention to use commuter rail, partly because of the long gaps between trains on weekends, but also because of the ridiculously high fares compared to the subway. I will say however that assuming service levels are returned to normal post-pandemic, most bus routes, especially the ones that provide the only access to a given region, tend to run frequently enough on weekends to be useful.
Finally, there's no need to write an essay about the MBTA services here - I'm an MBTA geek myself and I know all of that already (heck, I wouldn't suggest a transit-based event if I wasn't savvy with the transit system).