Is Palawan the best island for diving in the PI?....I dunno if I would agree with that statement since there are so many great places to dive here...but then again I've only dove in Coron (which was great and I'd go back in a heartbeat) and not the rest of Palawan. I'll be going to Puerto Princesa for the first time this coming weekend but I certainly know you will be able to dive Bohol in 10 days and still want to dive it some more. So my vote is for Bohol. From Alona Beach, I dove with Philippine Fun Divers. Philippine Island Divers comes highly recommended too.
and FWIW, my cousin had a chat with Christian Bautista and he said that he enjoys Bohol better than Palawan.
But then again if I had to choose the scenery to stay and wake up in for 10 days, I'd choose the beautiful wall cliffs and crystal clear coves of Palawan over Bohol.
I've trekked up to Northern Cebu from Cebu City, but not to Malapascua, only to Bantayan. But I will say that I'd rather do the commute to Bohol rather than Northern Cebu from Cebu City. It's a 2 hour fast ferry ride then a 25 min car ride to Panglao Island vs. a 2.5 hour bus/private car ride then a boat ride to the respective island. But then the diving is highly recommended in malapascua by many people here (I have never been).
Hope that provides some insight.