AU First level feats
True that AU gives an extra feat at first level, but then the AU classes tend to get less of an up-front class ability package compared to D&D classes. AU uses unrestricted multi-classing, and this system means that players are less likely to cherry-pick classes just to get the neat level 1 abilities, then forget about them
I would suggest that players who start with an AU class get the bonus feat, and those who start with a D&D class don't.
Further to what others have said, keep AU and D&D spellcasting classes seperate as regards spell lists and mechanics. AU casters are more flexible but their spells have less power, generally.
Some feats are different - AU has no Dodge, instead having Defensive Stance and Defensive Move (one vs. missile, one melee). Item Creation feats are more free-form in AU. AU moves all the "+2 in two skills" feats like Alertness, Crafty etc. into one feat - Skill Application, where you choose the two related feats (it's the same effect, just tidier, like efficient programming!).
I'd say go for the AU feats as the basis for all. Add in any D&D ones that you like. That won't unbalance things too much. Again you might wish to keep the magical feats seperate. AU uses Modify Magic feat to cover most metamagic options except Quicken, so that might require attention to stop AU casters getting about 6 feats for the cost of 1 compared to their D&D friends.
As far as the no-spellcasting classes go, no problem. The fighter even holds his own vs. the Warmain and Unfettered, being a sort of general purpose middle-man style of fighting.
