I've been freediving many spots in the Philippines, and have found that avoiding the so-called 'freediving spots' or famous spots was the best course.
Most recently I was diving on Apo Island
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which was great except for having to have a so-called guide, whom I left with my GF and swam out where I wanted to go. The guides are used to taking people to the tourist spots, which means high traffic.
On Apo Island the tourist spot is just south of the boat landing, so I went there first than told him we wanted to go north of the boat landing and it was much better, more fish, bigger fish, and better corals, and that area allows spearfishing. I think the best way to dive Apo is to stay on a resort there for a couple of nights and that way you are free of the 'guides'.
I dove Panglao Island, Bohol, Momo Beach was good
★★★★☆ · Beach
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Siquijor Island, this was a good spot
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Camiguin Island, several spots, I liked this one
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I have found the best way to find good spots, with few people is to ride around the island on a motorcycle, and when you see a spot, explore.
And avoid the common places with 'guides'
Moalboal, I liked this area
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I got an AirBnB on the beach and dove from there every morning,
I also went to sardine run
★★★★☆ · Tour operator
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which was not particularly impressive for regular divers who have seen that stuff all over the world, but worth a visit.
On Cebu, I saw the whale sharks, tons of people, and guides, but good for a one time visit.
But I liked these areas better:
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★★★★☆ · Port
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Again, just ride around and when you see a good looking spot, go for it.