Yes please, so much this. I have the same (well, worse) mess...
I would also like to specify that this should include the S1 built-in plugins. Why they are getting "special treatment" and always listed at the top makes no sense.
I suggest adding a "A-Z" button or something in the top right corner (where you have the wrench and plugin image toggle) for toggling this feature on/off, as some users might be perfectly happy with how it is now.
This, in my opinion, should just happen. The current mess is not user-friendly and slows down working inside of S1.