The first 3E game I played in, in college, the DM started houseruling right off the bat, fixing things that were obviously problematic, since they never would have worked in 2nd Edition, while adding in all the cool stuff that had accumulated from previous campaigns.
It was a catastrophe. "Multi-classing" that worked like gestalt-classing, fewer skills (since Non-Weapon Proficiencies were "just fine" and all those skills were "for munchkins"), facing rules, and a million other things to correct for "balance" because the DM had no idea how to look at the system as a whole, and instead starting tearing out whatever did not make sense to his intuitions.
And then there was the assassin. *Shudder.*
I'm going to wait a good long time before I start dreaming up houserules. If Rule 0 is "change what you don't like," Rule -1 is "the game designers might actually know what they're doing."