Right, my experience seems to be pretty different from what everyone else seems to have had.
From my running an AU party through DnD adventures it seems to me that AU parties are slightly underpowered compared to normal DnD. I'd be happy to explain why I think that happened later or in a different session, but it's unnecessary here. In the end, it seemed to me a wash, however, as AU characters get advantages that smart players can use to even the score.
The high spellcaster classes seem to me to actually be better balanced against their DnD counterparts as the spell list for AU, while flexible, is weaker.
Even the Magister has to work a little bit to catch up to the Wizard and Sorceror's ability to use 'exotic' spells without penalty or limitation.
I do have to agree with everyone else, however, that you should have AU characters only use spells, feats, and so forth that have been run through the AU books or that you have used the conversion rules to adjust.
In terms of crossovers, works very well with most classes, and some of the classes are an amazingly welcome addition to DnD.
I, honestly, have no idea how I or anyone in my party lived, without access to at least the first three levels of Akashic.