AAC seems to be getting larger attention, but the codec isn't the best thing for encoding your music. You're actually better off encoding to OGG or FLAC than EITHER of the two formats you're considering, but if you're looking for widespread functionality, you'll be better off encoding to MP3 and keeping AAC for your eyepod.
I have heard that Apple is/has made tunes encoded to AAC specific to ONE player, similar to WMA's "license", and crap like that would be enough to piss me off and encode to MP3 just in case my eyepod ever went CRAP. A backup for your music, if you will. Eventually, something WILL happen to your eyepod, and I can almost guarantee that contacting Apple will get you the "We're so sooory, but try as we might to care, we regret to tell you that you are SOL".