Does the pilot automatically turn on the A/C when defrost is selected? If car manufacturers went with your philosophy, then they would leave the A/C in the last selected mode and let those pesky drivers smarten up on their own... read the manual and all that jazz.
I only had an engine code once at about 2000 miles, no fault found and cleared by the dealer with no hiccups in the next 7xk+ miles. I intentionally put it into 4wd, by the lever, and I recall the drivetrain bound up and the 4wd icon wasn't flashing (lots of other lights were flashing), but I could be wrong. I'm not planning on pulling a fuse to check it.
4Runner is in the shop today for the airbag recall so I had to drive my wife's new Pilot. The ventilation controls work exactly as you'd expect: turn on defrost (any speed), then you can add recirc or A/C, or both, your option. It does exactly what you expect it to do based on your inputs, not something different like preventing recirc on some settings, or shutting it off on it's own.
So while the giant touch screen interface on the Pilot is truly atrociously abysmal (certainly expect better for >$50k) Honda got the function tree right on the air controls while Toyota got it very wrong. And that bad decision isn't common across all manufacturers, or even the next largest Japanese manufacturer.
And not to beat a dead horse but shutting off unrelated functionality when there's a problem is just bad design. No justification (i.e. it doesn't happen very often) can change that fact. Having to carry a code reader and knowing how to use it is a kludgey workaround that most owners wouldn't be capable of.
Will either of these issues prevent me from buying another Toyota? Not individually, but a list of 15 taken together, maybe - and my list of annoyances with the 5th gen is at least that long now. Hopefully someone at Toyota reads these forums and takes constructive criticism seriously.
Oh, and the Pilot also still has a separate heater core for the rear seats, just like the 3rd gen 4runner did. Another thing us longtime 4runer owners used to have and now don't. Like I said, I hope someone at Toyota is listening.