I've never really used any of the Avid consoles, never been a fan of Digidesign since they screwed PC users over on the Session 8 and that bias has stuck with me to their consoles as well. Didn't help any that I find Pro Tools to be about the worst possible DAW for theatre sound design work because of their years of refusal to have faster than real time rendering.
The using your Waves plug in thing is probably popular because so much of modern music production is reliant on some damn plug in or other to create the sound. And since so much music production is still done on Blow Tools it does kind of make sense that when you hit the road it's easier to use the same plug you used in the studio rather than trying to reinvent the wheel.
As for Digico, I didn't notice all that much need to use the mouse when I've sat at the console with mixers on shows. But then those shows are up and running and in my world once a show is open, you really only need faders, mutes and solos and you occasionally tweak a channel EQ. Also the one venue in town that uses SD9s has a keyboard and trackball below the desk on a slide out shelf.
I will say that venue has two SD9s and they have been running for about 2.5 years now and they have not had any issues that I'm aware of. I certainly would have heard if the consoles were unreliable, even though those are not venues I work in for the most part. Of course theatre venues are probably the most forgiving of spaces the consoles are likely to be used in. Very little bouncing around, not out in the heat, most days used for a few hours and then shut off and typically well taken care of.
And see... I rarely enjoy working on a Soundcraft. I've not used a Vi series desk either so I can not speak to that model. But I've used plenty of their analog desks and the smaller digital ones. They almost always turn me off with things that I just don't find to be very intuitive or well labeled. But they do usually sound pretty good.
But that's just me...