While I like it conceptually, I think a system of line heaviness would be unworkable in practice, at least outside of something like a dedicated bus map. The current system map is first and foremost a rapid transit map, with the key bus routes, the Commuter Rail, and the ferries as distinctly secondary elements, which is probably why the Silver Line's designation as rapid transit feels so out of place, because it's much closer to some of the bus routes (at least in places) than it is to the rapid transit lines (particularly the heavy rail lines). The problem, though, is that any line weighting system that reduces the weight of the RT lines (for the sake of clarity) unnecessarily and problematically deemphasizes the highest-capacity trunk lines, and any system that doesn't risks being fiddly and hard to distinguish. I imagine there's probably some way of threading that needle, though whether it'd be workable in all of the different sizes and conditions the map is reproduced in is hard to say.
I do like the idea of some kind of designation for the improved buses, like how the MTA in New York has the Select Bus Service with the SBS and + sign designators to set it apart from the normal buses. Something like that is probably more easily implementable. Ironically, the Silver Line designation itself is essentially serving that function for at least some of the "improved" routes, albeit given misleadingly equivalent emphasis to the proper RT lines (not entirely unlike the Green Line surface branches, which used to be treated differently on older maps). Of course, changing the Silver Line designation on Washington Street would mean admitting that it's not actually a proper replacement for the Elevated (while that's a plain and obvious truth, 'admitting' as much is probably not something any of the politicians want to have to deal with).