I've seen a couple of other D20 variant books (Swashbuckling Adventures comes immediately to mind) that would make for some serious changes if ported over directly into [fill in name of campaign setting here]. I don't find AU any more bothersome than these others.
When I picked up AU it was with the thought that I would be using it as a new primary book for a brand new campaign, bringing in elements from other volumes as seemed appropriate. This has proven to be the case. I am busily designing the new world and setting and looking through the 3.0 PHB and 3.5 SRD to see if there is anything from there that I want to port over, along with a number of splat books that I have picked up over time. This will end up including a fair number of feats, a few spells, and maybe a couple of prestige classes, but in the main, I would be using AU as my core book.
OTOH, placing the Oathsworn, Akashik, Unfettered, Warmain, and Champion into an on-going campaign would be very easy -- it's only when you are faced with magic that matters become trickier.
But then again, I have no strong tie to or interest in FR, Grayhawk, or any other "standard" setting, so in many ways my job is easier.
Personal opinions only, of course.