Things change almost monthly with ATA and SuperTrooper should really jump in with the latest. He's out on family vacation with no real Internet access, but I'll forward on this link.
The helmet for sure is different. AP is a smooth cap and back while ATA still retains bumpiness, even in ABS. ATA bought one set of helmet molds from TE2 (TE2 actually had two different helmt molds, but never offered the second one), so will soon be offering two versions of lids if he hasn't already.
ATA used to sell different right/left biceps but I think now has dropped the non-ANH left one and just sells two right biceps like AP. I have a set of ATA due to arrive any day and will have to check the forearms, but I suspect they may be different. I know the AP forearms have smaller rounder dimples on the outside, whereas TE2 has larger square ones. I suspect ATA will be the same.
Also, IIRC aren't there differences in the shins as well?
Lastly...AP has been around for ages and the armor holds up really well over time (at least it used too - not sure how his latest suits are being pulled). ATA also is very high quality. I don't think you can go wrong either way - it's just which small differences appeal to you.
Geez - used to be discussions were all between FX, RT, and AP/TE. How far we've come from a costuming standpoint that not people are sweating deltas between AP, ATA, T/MC,etc.