As blink* said, the two skimmers differ in design as to how the bubbles in the main chamber are generated.
The CPR uses a T connection and airhose to draw in air at the pump outlet (venturi driven).
The AquaC squirts/sprays the water from the tank into the chamber (like spraying a garden hose into a bucket).
Both work fine for smaller tanks. I've had both and found that they both work fine once they are set up and tuned. It does take a while for them to "break-in", and for adjusting the height of the collection cup. I think that the AquaC makes slightly better skimmate with fewer readjustments. The AquaC (with the paper towel mod) is also quieter than the CPR. However, it seems to be commonly accepted in the forums that the CPR needs to be cleaned regularly (bimonthly?) to maintain optimum results. I think I had fewer microbubbles with my CPR too.
Again, as blink* said, go for the in sump skimmers if you can. They can be cheaper (CSS) and work heads and tails better than the hang-on-back skimmers.
Hope that helps.