I'm not entirely sure I get your argument.

The MBTA faces a bunch of horrible infrastructure limitations:

1. Only two rails for all subway lines, so a lot of the maintenance requires downtime.

2. The green line is on horribly dated signaling mechanisms, and also has to deal with traffic at various points.

3. The commuter rail has terrible stations, often requiring a very long time boarding, and single tracks at many points.

Alot of that would make your operational complaints better. Sure, there are problems with the MBTA, but likely the solution isn't to avoid fixing anything.