I would say the differences are mainly cosmetic at the moment. AOKP has more native theme options built in (like built in weather in the pulldown menu), as well as a ton of easily modified themes available, from the GNex. CM9 seems to have far superior battery life, but if you're a power user like me, you've learned to always have a charging cable on-hand. I've found AOKP to be a bit quicker, and better at handling multitasking, but then again, I haven't used CM9 since Alpha 7, so I'm not entirely sure what kind of improvements have been made... I just like the overall feel of AOKP, and the tons of extra features (performance, theming, etc) that it offers.
I would say the worst case scenario...just use Safestrap, backup your stock rooted system, then flash either AOKP or CM9, test one for a day or two, then the other, and see which one you prefer. I'm doing that now with early MIUI builds...I never gave MIUI much of a chance back with my OG Droid, but I hear great things about it, so I'm testing to see if it's worth switching from AOKP, and Safestrap makes it quick, and well....safe, lol.
And no, you won't be able to flash a CM9 nightly directly over an AOKP nightly without wiping, since they're not the same code base, but if you don't mind the extra wiping and setting up of your device, then go for it.
D3 AOKP M4