Well, for me, it's just down to the representation of the mechanics. I own some White Wolf stuff, Synnibar *shudder*, D&D basic, Robotech, Recon, Shadowrun 2nd Ed, Maelstrom and D&D3.0. Have browsed through a few more. I started from by-the-book. That was when I was younger and the rules were just rules. Now, even though I've stopped playing, I'd really be doing a fair bit of house-ruling for most of these if I did start again.
Maybe I'm crazy but I find that I cannot accept mechanics if they don't give me a acceptable approximation of reality in terms of they work. Thus, as long as the system has stuff that I don't agree with, I'd house-rule it as much as I feel the need to.