This is coming from someone that actively uses and loves most features of mastercomfig so keep that in mind, however the two most clunky things about it in my opinion are transitioning to it and updating it.
I understand that the transitioning part has been made very easy by just moving files from /cfg to /cfg/user but I've had supposedly tech literate people struggle with this because they don't want to read a documentation, they want discoverability through use. I feel an installer of some sort would help this issue.
Having multiple VPKs is the biggest downside for me, it makes updating very clunky. I think this could be fixed by having one VPK containing everything and one configuration file similar to modules.cfg, maybe named something less scary and more intuitive like mastercomfig-settings.cfg, although I understand this comes with drawbacks.
With discoverability in mind, additional aliases for self describing cfg file names with a ready made cfg folder I think could help stop documentationphobic people from having difficulties. By this I mean you could have an alternative cfg for autoexec.cfg called something like run_on_game_launch.cfg, an alternative for game_overrides_once called run_on_server_join.cfg and so forth.