This RFC has a point but I'm confused about the scope: are you proposing these changes with all MediaWiki users in mind or are you focusing on the Wikimedia case? Consistency across Wikimedia sites is good and therefore setting limitations might be a good idea. However, the average MediaWiki site doesn't have problems like having different wikis with different admins not talking to each other, all under a same umbrella.
If the problem is to keep visual consistency across Wikimedia sites then the solution goes probably through a community agreement (like sticking to consistent logos or to the five pillars). Setting technical limitations without community agreements will just open the door to potentially uglier hacks in order to differentiate.
For a 3rd party MediaWiki admin, MediaWiki:Commons.css is a simple way to customize your site without moving away from Vector (arguably the only skin out there with a long term support guarantee) and without hacking directly the skin with changes that will be overridden in the next upgrade. Any changes to the current status should consider these two factors and offer something just as good or better.
About CSS bloat/abuse, what is the performance price for a wiki site? A default MediaWiki installation has already a jungle of CSS files with little to no documentation. Maybe a simple list of DOs and DONTs would help MediaWiki:Commons.css tweakers to do the right thing more than hardcoded limitations?