> with ever more insane checked bag fees (e.g. $25 on a $100 ticket!)
You probably know this, but to be fair, this is because they need to make a certain amount to have a viable busines, and an easy way to do that is to reduce ticket prices while increasing fees for other services. In the absence of checked bag fees (and assuming all else is equal) that hypothetical $100 ticket probably would have been closer to $125. But there is clearly a psychological difference.
> if you try to take a bag that is clearly too big onboard, they waive the fee at the gate which "punishes" the people responsible enough to check.
Yea that is a bit unfair. But it likely stems from the fact that airlines often end up gate-checking bags, once the overhead bins are full. If they enforced the bag check fees at the gate and had to measure every bag to decide if it should be free or charged, flights would be delayed and passengers would be (even more) unhappy.