Time of year recommendation: January to June or July. After that, you could be just fine and the diving could be just fine, or your number in the negative lottery might come up and your trip be spoiled by a typhoon. Stay away from Holy Week and book ahead if you might hit Golden Week.
Malapascua is lovely, and of course you do get to tick the thresher sharks and maybe mandarinfish off your life list. However, I'd return to Apo Island again and again for the stunning biodiversity and super-easy diving, while the same is not true of Malapascua. Puerto Galera also scores for novice/refresher diving whilst offering chances to add more challenge (interesting little wrecks, Verde Island).
In case, just in case, dear Muzzman, you and the missus are near my age bracket, I might mention that the boat transfers en route to Malapascua involve getting on to a little launch from the beach at Maya and transferring to a larger pump boat. Making that leap can be tricky if the sea is not calm. At the other end, it depends on tides: your pump boat may run up on to the beach for you, necessitating only a few steps down a plank, or you may have to do another leap to a small boat to get to shore. Same transfers may be involved in each dive, again depending on tides. Thank goodness for strong, helpful boatmen.
On reflection, you could interpret this as reason to go to Malapascua quick, before your knees get any older.
For a mere two week break, ease of transport is everything. So much travel within the Phils involves flying that trying to hit three places could keep you out of the water for four or five days, ptui!
Any of the following combos would minimize your travel time and offer great diving:
Puerto Galera (land/sea transfer from Manila 3-5 hours) with Bohol (fly Manila-Tagbilaran) or with Apo Island (fly Manila-Dumaguete, another couple of hours at most land/sea)
Malapascua with Moalboal (fly to Cebu, land transfers between the two), or with Apo Island (fast ferry or fly Cebu-Dumaguete), or with Bohol (fast ferry Cebu-Tagbilaran)
That liveaboard combo of PG / Apo Reef / Coron sounds like something I'll add to my next Phils dream and is also certainly doable in two weeks. With a third week, one could add Southern Leyte, which probably is less difficult to reach than I've been imagining.
Agree that El Nido diving is meh.