Mine would be the adherence to the 13/26 episodes per season rule. Yes I know if they didn't have a standard length it would be very annoying to schedule all the shows together with some kind of coherence, but so many shows lose something when they're either forced to condense what they have to say, or put in filler.
One of the reasons why I like anime so much better than anything America has produced is that the Japanese approach it with a "Here's the story we want to tell, and here's the time-frame to we'll tell it in", whereas in America it is "Here's our basic premise, how long can we add to it until it isn't popular anymore?"
Which thankfully saves them from having to leave shows open for extra seasons if it's popular, they can have more meaningful episodes. With shows like Time of Eve and Fooly Cooly, you can see just how much creativity they can pack into just how much time they want to have. So, if they got rid of the fixed number of episodes crap, it would get rid of a lot of the filler bullshit we have to put up with in 95% of shows, that waters down a lot of the good stuff.