OP simply fails to understand that fare basis (which underlies cost for both revenue and redemption tickets) changes constantly. It is a big world and a big airline. Availability changes all the time. Second to second. By way of example, had there been one seat left on the aircraft at one point, OP could not wait an hour and complain when someone else bought the seat.

His error and it is 100% his error was in not taking the upgrade offered simply because he could not select the seats he wanted. Had he done so, he would have had the cheapo upgrade all the way through and second, as the seats he wanted were still open, he could have made the change later. Third, even if not available, if you do not want anyone next to you: 1) fly private charter; 2) fly Suites; 3) buy 2 seats.

The change fee kerfuffle is just that. Deal with it sometime after the trip is done. Getting in a fight with an agent during a connection seems way over the top. Same thing with the amenity kit. Write in a note, "I got a seat for free and it wasn't worth it."