Ed,
I agree it is a pretty archaic limitation and I recently had to go through and exclude a bunch of Plugs after I purchased the Waves Gold Bundle. For clarification for those unfamiliar with Waves, Waves installs a Mono and Stereo (64-bit) VST and a Mono and Stereo (32-bit) version of the VST, so for every 1 Waves plug-in you install, there are typically 4 individual plugs associated with it. That can add up quickly. Simply re-arranging your Plug-In Menu does not rectify this issue. Personally, I need both 64 and 32 bit versions because I am using X2 64-bit for Mixing Audio, but I am still using 8.5 32-bit for MIDI as I prefer the workflow of 8.5 over X2 for MIDI. So the obvious solution may have been to go through and Exclude all the 32-bit Plugs;)
The Plug-In Manager is long overdue for an overall. I agree with you 100%......
Regards