Ok, after a week, I would say, unless it's due to the lower temps and rain, etc.. There's a definite improvement.
I now have a working theory, at least for my issues. Not saying it's right, but it's a guess: varnish/gum from oil in the intake settles around the throttle body and makes it harder to move than the motor is easily capable of when making small adjustments. You wouldn't notice this in a non-DBW car, because there, your foot moves the plate, and it's hard to tell that you need 2% more force today than yesterday.
As a result, the motor isn't easily equipped to deal with a much-harder-than-before-to-move plate, and lags terribly, stumbling around when first warming up. Once it gets freed a little bit, and/or warmed up, some of this goes away, and the car runs better. The fact that the car ran better if I floored/revved it up to 4500 in neutral once when it hit the bad part of the warmup cycle, seems to corroborate this.
Once you let the car sit for a while and the crud cools down, it gets harder to move again. One thing I did NOT know: if you put the ignition into "on" mode (but don't start the car!), if you press the accelerator, it will move the throttle plate. For obvious reasons, it's not as painless to do this once the car is running.
My suggestion for those suspecting this might be part of their problem: before starting, put the ignition to on, press/release the accelerator 5 times fully, and then start the car as normal. See if it makes a difference. If it does, it might be a dirty throttle body/plate.
I plan to try to clean it some more soon, but first I have a terrible rubbing noise to deal with. Appears to be brake rotor/pad related, since it always disappears if I lightly step on the brakes. Had a similar issue on the rear 2.5 years ago and new rotors/pads fixed it. This time it appears to be coming from driver's side front, but it's harder to pin down than I thought.
Honestly, brakes on this car (compared to my other cars: GLI/GTI/Corrado VR6 which get maybe 7-8/10 for everyday driving) are like 3/10. OEM warping/pad deposits, mushy pedal, etc, etc.. Subaru dropped the ball here, IMHO.