I did Bohol and Padre Burgos in October, 2012, including the ferry from Bohol to Maasin. Dove with Peter's Dive Resort in Padre Burgos. We were almost the only ones there - apparently whale shark season is the high season. First re the ferry - we got a ride arranged through the dive resort, Seaquest Dive Center, to the ferry terminal and got picked up at the other end by Peter's. Ferry ride was interesting - not very long, very smooth. Industrial ferry with big bay for trucks; passengers walk through this and up stairs to a deck with seats, two tvs (Philippine game shows - very garish!) and open sides. We were comfortable and all went smoothly. It was not expensive, though I don't remember exactly how much.
Regarding diving from Peter's. It was a bit variable. The best wall/reef diving was across the bay at the protected site - Napantao. We went back a couple times, even though it was a bit of a trip across Sogod Bay. We also went to some islands at the end of the bay - I didn't think those were worth the trip. The area south of the resort along the penninsula was interesting - sort of plain to start, but at the end there must be some upwelling, because we would get small-medium size schools of large fish. If I did that again I would want to start farther toward that end, so that I could stay a little deeper for a little longer - when it's at the end of the dive it's hard to stick at 50 feet or more. Also - the PIER at the town for night diving was absolutely amazing! They limit the nights you can go - MWF, I think - go as many times as you can! It's a fun spot topside - there is a video karaoke place you can hear as you go in; families eating take-out on the pier, and even people loading boats by carrying things down the stairs and into the water/onto the boat. Once you get in, sandy bottom with amazing critters, and the pilings are totally covered with all sorts of crabs, seahorses, corals, etc. Saw a huge turtle (woke him up - sorry!) and after the pilings, out in the sand are lionfish and stargazers. AND, north of the resort, there is a muck site - you have to walk through a trashy area on the shore (and in the water for a little ways) but it's a great muck site (I've done Lembeh, so have some perspective) with more seahorses, sea robins, guynards, pipefish, interesting anemones, etc - and there are some coral bommies there as well. There are definitely some plain/damaged coral areas - what I've described are the highlights - and I think there are enough to make it a good value and a fun place. The food was good and the accommodations very nice - pictures accurately show the resort, though the back is right up to the road (not too much noise.) Dive guides were good, pleasant, and other staff very nice. If you want more info/link to pics, let me know.