1st, big thanks for fixing environment vars and other bugs in build 0.9.12!
As for the suggestions. Currently NRI add-ons can be installed in one click. They actually copied to user dir and each NRA is added to common xml config file. For consistency, the is has to be a way to remove whole NRI (as it may contain a dozen NRA items) package in similar way. Currently we have to remove each containing NRA one-by-one. It's good and gives a user a way to remove unused items (customization), but IMHO should be combined with a button to remove entire NRI package as well. Also, in the later case, entire GUID directory of the NRI package should be deleted from user's add-on directory.
Possible alternative way may be allowing users to directly manipulate common xml config file (or/and via NRExplorer UI), so the installation packages will not have their own GUID and directory and every NRA can be freely moved up/down in the single NRA list. AFAIK there are none of version checking mechanisms implemented on either individual .nra or .nri package levels yet.