I concur that Option 2 would give you a greater variety of diving. I've made trips similar to this though and at least for me it was quite exhausting. Possibly because I did use public transportation for most of it 
Back in March I did Puerto Galera, Subic Bay, Moalboal, and Malapascua over about a 2 1/2 week period. I was traveling with a friend who, like you, wanted to see as much as possible.
I personally usually like to stay longer at a particular destination and dive more, but I'm retired and can take as much time as I want now unless I'm taking someone around
Your time in Malapascua is about right. There is not a guarantee of seeing thresher sharks (they are wild animals and conditions can affect sightings so anyone who promises I'd be careful of) but with 5 dive days there I'd be surprised if you didn't see them. You'll also want to do day trips to Gato Island and Kalanggaman Island while you're there.
A driver from the airport to Maya on the day you arrive would be a good idea. Might not make it in time for the ferry if you take the bus. You will definitely want to arrange a driver if you want to go from Maya to Moalboal in one day! That's a really LONG day by bus Your dive op can help you with all of that. When I traveled from Moalboal to Malapascua back in March we broke that up into two days, but we were going by bus and decided not to kill ourselves getting there. 9-10 hours on a non-air-conditioned, oftentimes standing room only bus can be exhausting
When I go to Malapascua I dive with Evolution. I've made I think 6 trips there now and 5 of those I dived with Evolution. Must be a reason I keep using them Matt and David have a great staff there and I've always been well taken care of. (You'll find everyone has they're favorites so just do your research and pick who you think you'll be happy with).
In Moalboal I've dived with Nelson's and stayed next door at Eve's Kiosk all 3 times that I've been there. I've found their prices to be quite reasonable. I like Moalboal and could easily spend 3-4 days there, but having said that you can see what you want in one day. Pescador Island in the morning and then be sure to tell them you want to see the Sardines. Those are the big draws there. You also commonly see turtles and occasionally even whale sharks and thresher sharks are spotted there.
In Dauin since you only have 2 dive days you will have to choose between diving Apo Island or Siquijor Island. Last time I was there in April I dived with Andre "Snoopy" Montenegro who's new dive op is called "Housereef Dumaguete". They run a bed and breakfast at their main dive shop where they also have a pool. If they're full they can make suggestions and help you get something set up. They can be found on Facebook and the web. I definitely saved money by staying in Dumaguete and just letting them take me out to Dauin each day
If you want the above water sightseeing you'll need the extra day in Bohol to go see the Chocolate Hills, Tarsiers, zipline, etc... If you add a day I'd suggest doing it in Dauin so you can do the side trip to Siquijor Island. I've been to all these places except Siquijor which I've heard good things about. I expect to be in Dauin for at least 3 weeks when I head back to the Philippines in a couple of months and I definitely plan a trip to Siquijor next time I'm down that way.
I wouldn't really consider option 3 since maximizing what you see is important to you. If you have any questions shoot me a me a PM and I'll help you if I can. I'm sure you will have a great trip no matter how you finally decide to structure it
If you want to read more about some of these destinations just click on the link in my signature and it will take you to my blog
Back in March I did Puerto Galera, Subic Bay, Moalboal, and Malapascua over about a 2 1/2 week period. I was traveling with a friend who, like you, wanted to see as much as possible.I personally usually like to stay longer at a particular destination and dive more, but I'm retired and can take as much time as I want now unless I'm taking someone around
Your time in Malapascua is about right. There is not a guarantee of seeing thresher sharks (they are wild animals and conditions can affect sightings so anyone who promises I'd be careful of) but with 5 dive days there I'd be surprised if you didn't see them. You'll also want to do day trips to Gato Island and Kalanggaman Island while you're there.
A driver from the airport to Maya on the day you arrive would be a good idea. Might not make it in time for the ferry if you take the bus. You will definitely want to arrange a driver if you want to go from Maya to Moalboal in one day! That's a really LONG day by bus
Your dive op can help you with all of that. When I traveled from Moalboal to Malapascua back in March we broke that up into two days, but we were going by bus and decided not to kill ourselves getting there. 9-10 hours on a non-air-conditioned, oftentimes standing room only bus can be exhausting When I go to Malapascua I dive with Evolution. I've made I think 6 trips there now and 5 of those I dived with Evolution. Must be a reason I keep using them
Matt and David have a great staff there and I've always been well taken care of. (You'll find everyone has they're favorites so just do your research and pick who you think you'll be happy with).In Moalboal I've dived with Nelson's and stayed next door at Eve's Kiosk all 3 times that I've been there. I've found their prices to be quite reasonable. I like Moalboal and could easily spend 3-4 days there, but having said that you can see what you want in one day. Pescador Island in the morning and then be sure to tell them you want to see the Sardines. Those are the big draws there. You also commonly see turtles and occasionally even whale sharks and thresher sharks are spotted there.
In Dauin since you only have 2 dive days you will have to choose between diving Apo Island or Siquijor Island. Last time I was there in April I dived with Andre "Snoopy" Montenegro who's new dive op is called "Housereef Dumaguete". They run a bed and breakfast at their main dive shop where they also have a pool. If they're full they can make suggestions and help you get something set up. They can be found on Facebook and the web. I definitely saved money by staying in Dumaguete and just letting them take me out to Dauin each day
If you want the above water sightseeing you'll need the extra day in Bohol to go see the Chocolate Hills, Tarsiers, zipline, etc... If you add a day I'd suggest doing it in Dauin so you can do the side trip to Siquijor Island. I've been to all these places except Siquijor which I've heard good things about. I expect to be in Dauin for at least 3 weeks when I head back to the Philippines in a couple of months and I definitely plan a trip to Siquijor next time I'm down that way.
I wouldn't really consider option 3 since maximizing what you see is important to you. If you have any questions shoot me a me a PM and I'll help you if I can. I'm sure you will have a great trip no matter how you finally decide to structure it
If you want to read more about some of these destinations just click on the link in my signature and it will take you to my blog
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