Hi,
I have experience with both brands and they are both good units with a strong outputs and good customer support. When it's time for a replacement cell, the OEM Hayward cell is less expensive than the OEM Auto Pilot cell. Curiously though, the generic Auto Pilot cells are cheaper than those for Hayward. Also, the AquaRites are so common, you can get many of the electronic parts online. As for AutoPilot, it's a pleasure to deal with their factory people...very responsive to whatever you need.
Pick whichever one suits your fancy. You can't go wrong.
Don