Got back two days ago...just wanted to say a big thanks to everyone who helped provide insight for me. Here's a trip report/summary:
First 6 days we spent in Alona Beach on Panglao Island, just off Bohol. 6 days felt like a good amount of time to get a good combination of diving/exploring on land. Alona Beach had some good restaurants (Bar Woo was my favorite) but the area itself isn't very pretty and is a hot mess with traffic and pedestrians everywhere. Nothing awful, but might as well stay in a nicer/more laid back area if you're visiting the Philippines. If I could redo it, I'd do 3 nights in Alona Beach, and 3 nights in a different area or further inland in Bohol.
Diving--Balicasag was fantastic...make sure you have a dive shop reserve permits for you far in advance. Only 150 diver permits are issued daily, and everywhere was booked up far in advance when we got there. I was glad I had communicated that I wanted to dive Balicasag so a permit was held for me on the first day when I arrived, but I had a hard time finding another day and lucked out when there was a cancellation. At Balicasag the water was a little chilly (24-25 Celsius) but visibility was very good and the school of jack fish was pretty awesome. Also saw big schools of fusilier and big mouth mackerel. Really pretty reef top too. Local dives were pretty underwhelming, although a quick dive at Danao Reef was very nice.
Dive Shop: Dove 2 days with Tropical Alona and would definitely NOT recommend this company. I don't want to make this post too ranty/negative, but I'd strongly advise going with a different company based on my experience. Happy to share details in a PM.
3rd day we dove with Prana Divers since they were the only one we could find with openings at Balicasag. The owner was pretty condescending (he seemed personally offended that I wanted to try on fins/mask to make sure they fit me before diving), but the guides were great and the dive shop seemed smooth and efficient.
Also worth noting, we had great sardine snorkeling a little bit north west of alona beach at Napaling Point. Easy to get to via 20 minute motorbike rode. Bohol was awesome
Next part of our trip we went to Malapascua and had a fantastic time. We stayed at Evolution and I found this resort to be top notch in all areas. Great guides, very hospitable atmosphere and an overall social and friendly dive shop. We did 9 dives in total here. 2 thresher shark dives....one was murky but we got a great view of 1 at the end. The 2nd dive we saw probably 10-15 with perfect visibility, it was just incredible. They are stunning in person and this was the highlight of Malapascua by far. We did day trips to Gato and Kalangaman as well. Gato was great for white tips and we saw some cool macro stuff but the sites were too crowded IMO and too many people trying to take turns seeing tiny things. Water was cold as well. Kalangaman was nice overall, great coral gardens in the shallow area and then a sharp and very deep drop off. Almost zero current and the wall was pretty underwhelming (cold and spent too much time pointing out nudis that no one was too excited by) but the 2nd dive we spent the bulk of our time in the warmer shallower area which featured some great coral beds. We did 2 night dives as well. One was at Chocolate Island, I had issues with my torch which basically ruined the dive but the area was quite beautiful. Visibility was awful though and it was quite cold. The first night dive was a local site and overall I found it somewhat underwhelming but loved seeing a flamboyant cuttlefish and some other cool creatures. The night dives paled compared to the others I've done in Bunaken and Lembeh but were fine. We spent 5 nights/4 days here and would've been fine shortening it to 4/3, but enjoyed the full time here. There really isn't anything to do besides dive and the best stuff we saw was at Monad Shoal (threshers) and Gato Island. Cannot recommend evolution enough though. We each spent about $130/day which included a room with ac, 2 dives, equipment, all meals and tips. The restaurant was fantastic as well....try the mac and cheese if you go.
Last spot we stopped in was Moalboal. Just did 1 day of diving here, although I wish we spent 2-3 days there. The sardines were pretty awesome. The first morning we dove with Cebu Dive Centre. Insanely cheap diving (about $15 for a shore dive, $22 for a boat dive) and equipment all seemed in good condition. The owner and staff were extremely friendly and checked in with us before/after diving. The boat dive we did was at Pescador Island which was pretty spectacular but we had very strong current and our guide was pretty awful....we had to swim into a strong current and drop down about 25-30 meters right off the bat and he didn't brief us at all for it. When he told us to descend, he immediately descended and just took off swimming very fast into the current. He didn't check in with us to make sure were descending okay, nor did he check to see if we were following him for the first 5-10 min, he just took off and we had trouble keeping up. Everyone in our group went through about 50-60 PSI right off the bat and honestly I didn't feel safe since I could barely see the guide and my dive buddy (who's my best friend) was struggling to keep up behind me...wasn't sure what to do at that point but I stayed with my friend until we eventually caught up a few minutes later. A little bit of preparation/briefing would've gone a long way. Especially since after the dive, they told us the current had been quite strong the last few days due to the full moon so they were expecting it. At any rate, Pescador Island was absolutely STUNNING from what I saw. Would love to go back when the current isn't as strong and do at least a couple of dives there. Pretty awesome spot. Saw barracuda, some massive grouper, a zillion gorgeous reef fish and the vis was crystal clear. Definitely better reefs there than what we saw in Malapascua. The next dive was at Tongo Point? which we skipped but were told by other divers that it was underwhelming compared to Pescador.
The town of Moalboal was fine but nothing to write home about. We did a day trip to Kawasan Falls nearby and it was one of the best activities of the trip. There's a lot to do in the area so I would've spent more than 2 days there in hindsight.
If I were to redo this trip, I'd probably spend:
5 days in Bohol
a day of travel to Malapascua (2 hr boat ride and 3.5 hour drive)
4 days at Malapascua
Day of travel (5 hr drive)
3 days in Moalboal area drive back to Cebu at night (2-3 hour drive)
Also worth noting--Cebu traffic can be horrendous. Even on a Sunday night it took us about an hour to cross from Cebu to Mactan. We were lucky and had our travel days on Saturdays and Sundays, apparently it is MUCH worse during the week so I'd recommend planning your travel days around this schedule if you're passing through Cebu City. Also make sure you check moon cycle info when planning your trip, wish i had in hindsight. Overall though it was a fantastic trip and I'd 100% recommend visiting the Philippines if you're considering it.