I'm totally with you for EVERY point about the plugin manager.
I'd add bi-directionality to the Media Browswer, so I can quickly work library items back and forth.
Independent timeline for the Matrix View would be nice.
ACT 2.0! (or something, fer realz this featureset needs some lovin')
Audiosnap 3.0! (they've done a lot of work here, but it's still needs more integration and a more intuitive workflow for beat-mapping functions)
VARISPEED!(my biggest "I want a pony!" desire)
Smoother, more instant screenset transitions
"Replace Synth" command, with some allowance for a newer version of the same synth to be able to read patch selection of the replaced synth.
A "smart select" where selecting the MIDI track of a soft synth will intuit that the audio track is assumed when doing bounces and exports.
Custom control bar modules with a wider access to functions.
Exposing all plugins and audio tracks to inputs would be rad. So we can finally do live recording (bouncing) from bus-to-track and such. I'm a big proponent of SONAR's bussing structure but it's been a while and having some way to do live bounces without going out and back in would be faster workflow.
V-Vocal integration into the Track View. Someone has to say it: the V-Vocal UI is a bear to deal with, and without being able to see multiple tracks or otherwise have visual cues it's a chore to do detailed time-based editing. Everyone else is working it into their core interface, I think it's time to make the jump (this could probably be merged with Audiosnap and/or varispeed updates as well)