My liveaboard experiences have only been on some of the "rustic" style boats. We did 2 trips on the non-defunked Nekton. Loved both trips, wish they were still around. We did a trip on the Eco Explorer in Palau (not part of the Explorer fleet, but part of a group owned by a Philippine company) which we really enjoyed though the boat was a dump. We have also done numerous 2-3 days trips on liveaboards in Calif, which have bunkbed open rooms below deck and only 2-3 restrooms for whole boat of 30+ people. Yes, we have really survived that and LOVED it.
So it all depends what you want and where you are going.
In Calif, there is no real other choice or way to get out to outer Channel Islands for multiple days. Worth the hassle and lack of privacy, as well as the wait to pee.
In Palau we had to choice of several different liveaboards, but went with the EE, and really enjoyed it, mostly because we loved the crew, the food, the other divers, and the coolness of being on such a funky old whaling ship.
In Caribbean, we did the Nekton... not luxury, but not a real dump either. Great crews, great food, great fun people for a week.
We have not splurged and done an Aggressor or Hughes boat, but we do talk about it often. It is expensive for us, so we debate on it. Not sure IF we will ever go, but I am very interested in trying a trip to Belize or Caymans on one of those boats. The Explorer also has boats in the Caribbean, but we haven't tried them yet either, nor have we tried the AquaCat, for no particular reason other than time and money. If I had my way, I would book one of these for this summer.....
robin