Having dove Palau with both Aggressor and Ocean Hunter I can certainly give you a comparison of the two.
First of all, you really can't go wrong with either ship. They're both in excellent condition and the crews are fantastic. The diving speaks for itself.
The skiff setup on the Aggressor is better. It actually sits on a cradle at the back of the ship and is raised up to deck height after each dive. Your tanks and dive gear never leave the skiff. Your BC stays attached and you dive the same tank all week. Getting the skiff up and out of the water means they can move faster when necessary.
The Ocean Hunter basically tows their skiff behind. It works, but it's a bit clumsy. Tanks are sometimes filled aboard the skiff, sometimes swapped out. The deck showers are in the WORST location on the Ocean Hunter. They're right at the rail opening where divers walk off of the skiff and onto the main deck. It makes the starboard shower all but useless. In addition, all of the wetsuits are hung together in a small location on the port side of the ship. It's mostly one person at a time going there to pull down a wetsuit.
That said, you will get more dives in during a week aboard the Ocean Hunter. They do a short turnaround so you get a few more dives.
I'm sure I'll dive Palau again and really, I'd just flip a coin between the two. It's about the diving anyway and that's nothing short of spectacular.
-Charles