I dived Malapascua 15 years ago, seen the threshers, seen the mantas and that's about it.
I ddin't go back to Malapascua because I was not impressed with the rest and thought it didn' have the array of diving some other places have.
I didn't dive with Sea Explorers but with Exotic island, both have been there for a while..
In the meantime I came back 5 or 6 times to Alona with Sea Explorers or PFD, so yes it has been going downhill (I don't know of any dive destination that has been improving for the last 20 years...) but not to the point I won't be coming back. There's still a lot to see underwater (I have photos to prove what I'm saying, you can browse my flickr galeries
).
I understand your point on a honeymoon that said there are two different options in this case, either go out to restaurants or stay comfy in a very quiet place.
I am traveling with my non diving wife and she appriciates much more somewhere with places to go out than staying on a small island and nothing to around (Ajthough she loves Raja Ampat mind you, but because nature is beautiful there, unlike on a flat island). You will certainly find more comfort and activities on Alona than iin Malapascua, If you want spacious willas at affirvdable price try Kasadya I mentioned above, if you want to indulge yourself in Luxury there's Amorita resort.
Now if you are looking for more quietness in a comfortable place with a very flexible dive centre taht will taylor your dives to your needs, I can also recommend Cabilao Sanctuary Beach Resort near to Panglao and VERY easy access from Cebu city.
I wrote up a report about those destinations, browse this board and you will find it.