I was just in Palau in November, on the Palau Aggressor II. We didn't do land-based at all, but one of the other couples on our boat said they did a land-based Palau trip a couple years earlier and much preferred the liveaboard. Although you can visit most of the same sites via land-based, you spend a lot more time in a small boat and can't fit in as many dives a day.
The Palau Aggressor II was exceptional, in my opinion. The boat appeared to have been renovated recently - the carpet in the cabins looked brand new and everything worked as it should. It was also the most stable boat I've ever been on (it's a catamaran) and the crew were excellent.
If I was going again (and I hope to one day), I would definitely go liveaboard again. In addition to the factors above, I enjoy the camaraderie of liveaboards. But no matter who you you dive with or where you stay, I don't think you can go wrong with Palau - it's the best diving I've done.
James