I disagree with your perspective - chances are you cut it too close, so the passenger certainly has part of the blame but if EZ Check In wasn't working, then UA has a share. Also, if it really was close on time, I would've foregone the upgrade and taking a bp just to get through security and dealt with it at the gate.
You're a 1K so get free confirmed on next flight w/i 4 hours - not sure why the change fee, that would depend on how long till the next flight and how full it was, etc. What was the routing and how much time between flights?
Baggage rules are joke ... nothing more to say on that one.
As a 1K - may I ask why you just didn't do OLCI? Even if you can't print it out at least you're checked in so the upgrade is taken care of, etc in advance.