We've stayed at both and honestly, I really liked both, which I know is basically no help. They both had their +/-...
Transportation: Both only offer bus transportation, so neither really wins out over the other. That's why AKL tends to be the "cheapest" deluxe. Personal experience, the buses at CBR were a lot faster/better than our experience at AKL.
Distance: CBR wins. I felt like we were on the bus for forever with AKL, especially given the wait times for the actual buses. 9/10 times we were on a 2 bus deep line waiting for an AKL bus to show up (which could have just been a fluke experience).
Pool: I heard a lot of great things about the AKL pool and I am the TOTAL minority here, but I was a little underwhelmed by it after hearing such amazing things. I actually liked CBR pool better.
Rooms/Resort: I prefer the layout of AKL (where you're in the one building) vs. the spread out feel. We had no complaints with either room, with obviously AKL's being a bit nicer. We rented points at AKL, so we were on the top floor (5th floor) and our "standard" view ended up being a re-classified Savannah view, so we can now never stay there without the savannah view. Lesson learned: it's worth it, and honestly, the total appeal of the hotel. It was WONDERFUL seeing the animals from our private balcony, and I can't imagine staying there without it. However, if you don't spend for the upgrade, you can see animals from around the hotel, which is a plus. But really, it's worth the upgrade. Total cool factor. Inside AKL is beautiful. We really felt like we were at an African lodge. However, being at CBR we also felt like we were at some tropical oasis.
Dining: AKL wins. It has deluxe dining amenities (room service, more restaurants, etc), so that wins for us. Jiko ended up being one of our all time favorite Disney meals, which I would have never gone to if we didn't stay at AKL because it's SO FAR.