Hussar
Legend
If the rules are causing problems and you need to throw them out, isn't that kinda proof that the game is heavily flawed?
The answer then is to discuss those flaws so they can be remedied in the next game or the next edition or what have you.
Well, no, not necessarily. It might simply be that the rules are fairly complex and detailed, but don't come up all the time. As was mentioned, tripping in 3e or ((shudder)) grapple. Or, it could be something really situational. After all, how often do you look up the balance rules in 3e? We rarely did. But, there were the odd situation where it might come up.
Flying combat rules are another one. Flying combat isn't something that came up regularly in my games, so, when it did, we typically had to break out the books to figure out if we were doing things right or not. I can see simply handwaving it for the sake of expediency.
Although, as I've become older and hopefully a better DM, I almost always handwave in favour of the players now.