This part of your proposal does interest me. Not necessarily the details, but the concept that Factions, Classes, and Ships should all have advantages and disadvantages that can be mixed and matched to some degree to specialize.
However, I forsee huge implications for PvP and I'm not sure this would be acceptable to the PvP community.
The part of the proposal that you quoted depends on Romulans being made an INDEPENDENT faction in order to make it work... as intended ...which is why the rest of it is in here.
The details of implementing it would be up to Cryptic, of course, but the concept is what I am trying to illustrate here.
And as far as PvP goes, one of the points of this concept IS to have an impact on PvP. And I would think the PvP community would enjoy the challenge of discovering new builds, new combinations, new possibilities to use in PvP.