Amtrak's engine changes at New Haven and Washington are typically scheduled in the 20-30 minute range, but I'm not sure it really takes that long, I think some of it is just schedule slop/padding before venturing out onto single track lines where they want to be more on schedule.
Interestingly, the ability to make and break EMU consists isn't exactly a major selling point for EMU operations. Generally, MN just runs larger sets and doesn't make and break them and still benefits from all of the other benefits of EMUs.
Diesel push/pull is the slowest and dirtiest way to run a commuter train, and should only be used for a handful of long and thin routes like the Old Colony and Greenbush lines. But with electrics, if you put enough horsepower, you can get close to EMU performance, although EMUs are the king performance wise, assuming they have adequate traction power. LIRR has many areas that don't, so they run their EMUs at half acceleration, and MN has areas limited to only 6 cars, whereas MBTA would be running on 25kV AC, so that should help to be able to run them at full acceleration speed with full length trainsets.
Generally, single level cars make a lot more sense than multilevel cars, except in the most capacity constrained runs, due to less dwell time at each station. But as a transition, I think it would make sense for MBTA to operate with loco-hauled push-pull, at least for a while, as they phase in single level EMUs, and figure out where each design makes sense. There may be some routes where the MBTA double decker coach design is necessary to support ridership, and where they could be run with 8-12 cars with two locomotives providing decent acceleration.
Due to the need to electrify in order to build the North-South rail link, all lines except Greenbush and the Old Colony Lines should be fully electrified, allowing for one smoothly running system that runs through the rail link, and then separate above ground trackage for Greenbush and Old Colony, as well as Amtrak trains terminating at South Station.
The reliability discussion is puzzling, as electric with EMUs is WAY more reliable than diesel. Yes, it occasionally fails, but redundancy can be built into the design of the system, as it is with Amtrak's Shore Line traction power system. Diesels fail all the time, there's just way more to fail, and a single-locomotive electric push-pull would be somewhere in the middle.
Except for weird fringe cases where seasonal or low-volume service is provided, platform height and length standardization should be done across all commuter rail lines. Naturally, this is mostly only a problem in the Northeast, as everywhere else uses low-level platforms, and they are generally easier and cheaper to make longer. In the MBTA's case, standardization of length for high-level platforms as was done with Old Colony and Greenbush makes total sense, and would further improve the schedules with less dwell time.