All else being equal I have a slight preference for Aggressor due to food and atmosphere, but the 2 are really similar enough that I would choose based on destination, and also on the quality of the individual boat. (They have both over the years had boats in their fleets ranging from really nice to "should have been retired already." I think there's been more range in the quality of Aggressor boats, but then they've got more boats and all that matters anyway is the specific boat you're going on.)
Even if they've got nice boats in the same place, they can be pretty different. For instance, I've been on the Sun Dancer in Belize several times and toured the Belize Aggressor, and slightly prefer the Sun Dancer due to nicer cabins and inside areas, though I liked some other things better about the Belize Aggressor. I suppose that one is pretty much a wash. In Fiji, the Aggressor and the Island Dancer (badged Aggressor until recently) are very different boats in size and type - Aggressor is a larger cat with I believe more diving from the tender, and the Island Dancer is a smaller monohull with fewer passengers and more diving off the main boat. If more than one boat operates in the same area you might also look at the actual itinerary if they're significantly different.
There's minor differences in the way Peter Hughes and Aggressor operate day to day. Like Peter Hughes does a bit more of the fluffy bathrobe, neck rubs after the dive, stuff like that and the crew wears uniforms for dinner which is served sit down. Aggressor dinners I've seen are mostly buffet and the crew will be in the usual t-shirts, giving some people the impression that PH is more "formal" - though it's really not and wearing the fluffy bathrobe to dinner would be ok. From the boats I've been on I've tended to prefer the food and buffets on the Aggressors over PH.
Depending where you're thinking of going there's many other liveaboards in the same general class worth checking out. Simple availability is also a big issue, some of the boats will book up far ahead and that may make your decision for you.