WAI Improvements

As you have correctly mentioned at the beginning, WAI is just an indicator. So, with that in mind:
 
1) can be implemented inside Sonar. In case Control Surface plug-in does not change its location on load.
 
2) there is a trick:
 a) unset "Keep track/console visibility in sync" option,
 b) in the Control Surfaces property, select "Control Strips Visible in": "Console View".
 c) hide some track in Console view.
Your Track view has "WAI gaps" now and Control Surface only "see" not hidden in console tracks. You still can see and operate all tracks in the Tracks view.
 
For "Folders", you can select "... Visible in" "Track View". Once the folder is closed, tracks in the folder are excluded from WAI.
 
It is possible to hide MIDI tracks in the "Track View", but I normally prefer to see MIDI clips...
 
Warning: there are some bugs when using that approach. In WAI indication, Track Inspector, etc. But there are more for "bug report" and not for "feature request".

Brando
Regarding 1, are you saying that I should have the capability within sonar to do what I need now (in which case I'm doing something wrong), or just that it isn't an ACT/control surface issue and should work in sonar?

Unfortunately not. What I means is that it can/should be implemented inside Sonar and once done will work for existing plug-ins.
 
Control Surface support in Sonar has 2 parts, one is inside Sonar and another is inside plug-ins. In case some feature is implemented inside Sonar that does not make it automatically available for end users  (concrete devices) till either corresponding plug-in is also modified on the change is not "visible" from plug-in side. A good example for the first scenario is ProChannel support. API (partially) support ProChannel control, but old plug-ins (MCU) should be modified to use that.
 
So, my post was just a confirmation that both your requests can be implemented as a "generic" modification inside Sonar part and modification of all plug-ins is not required (and so the probability that will be done is greater then zero...).
 
MIDI skipping (but not Folders, since as many other "new" features there is nothing in CS API to work with them) can be done inside particular plug-ins as well (my plug-in support that...), but I prefer to see it on Sonar side because plug-in is not able to inform Sonar about gaps in WAI (the only parameters are the "first" WAI track and the "width").