I took an AA flight from SAN to ORD Tuesday that looped up through
Utah and Wyoming, maybe to catch strong upper winds. But I got to
wondering how airline flight plans get planned. Does the pilot do
this, or the airline?

I presume that ATC overrides theirs as they do mine from time to time,
though the airlines probably have a better idea of what's likely to be
approved.

If you want to see the route, you can find it on Flightaware, AA1484,
Feb 20.