I have a mountain of changes I put in. lots are variant rules I've seen in one place or another, that I use to replace the standard mechanics.
Is it "fair" to the players: Yeah, I think so, I tell them I have alot of houserules, and if they don't like it they can find another game. Plus, if I have to play in people's games using the core rules with lots of mechanics I *DONT* like, then I'm going to at least run my games with mechanics I *DO* like.
A much harder thing, is trying to convince other GMs to run games and include your houserules. Trust me, I've tried. I few houserules catch on, but not all of them.
Almost all the d20 GMs I know use a few alternate rules I came up with for character generation and leveling, but they scrap alot of the other things I change. Most of the time because they don't want to try to remember what is in the published core book and what's been changed.