Aron: Will you have a chance to directly compare these two players in a store or at home? This would be preferable, but it's not always possible I realize. Having heard Wadia and Audio Aero extensively, I feel that they are both outstanding musically, but have distinct personalities that will rub each person differently. It's always hard to describe, but my ears tell me the following: In the midrange, Wadia has superb accuracy in timbre and dynamics, while the AA has that nice warm 3-D realism found in tube gear. In the bass the Wadia is clearly more defined, whereas the AA is a bit on the ripe side (the MKII is said to improve upon this). In the upper mids and treble the AA is smoother and slightly less extended than Wadia. This comes across initially as less transparency in the AA, but over time it is less fatiguing. (Wadia can be made much smoother up top via the Great Northern Sound mods.) I suspect that your final opinion will partly depend on where you fit in the "yin-yang" spectrum, or in the solid-state v. tube spectrum. I'd bet that Wadia tends to be prefered by many in the SS/detail/speed camp, and AA by the tube/organic camp. Huge generalizations I know, but maybe that's a first approximation.
Other things I've found: Wadia sounds nice run through tube amps, while the AA sounds nice run through SS amps (sort of balances out the character of the CD players). BOTH CD players sound more palpable without an active line stage, IMO. (Especially true for the AA.)
So in conclusion, do whatever you can to borrow the two units to try out in your system. Good luck!