Its not issue. Its how the functionality are made and programed.
I get it now why it is that way. There are a good reason why Steinberg implemented it that way if you haven’t notice that yet in Cubase 7.5. 
By the way… when I’m on the mixer-page on my second monitor I never lost connection to it as you describe?
I use pre programed hardware “softkeys” too to control the mixer functions and all work with no issues.
Many of the issues you describe and experience ,I’m afraid I don’t have them on my setup…
link channels etc work etc… Sometimes I use key command for that too…
Multi monitor environment here too= no problems.
organize the plugins? = Use in “preference” organize as “Vendors”. and the new “search function” in the plugin window couldn’t be easier. I use it every day.
Example want “Waves CLA plugins”. Write “CL” in the search field ------> …and "BOOM "CLA-Compressors comes up automatically.
Write—> Me… and “Melodyne” comes up… How hard can it be?
Work with it… not against it!
Best Regards
Freddie