Hi Andy,
I've been to both a couple of times, most recently to Malapascua last month. Phuket's major advantage is the nightlife, variety of restaraunts, and many other things to do besides diving. Malapascua is a small island feel with several places to eat but which only a couple are really good (Angelinas, Oscars), but not too much to do but dive or sit on the nice beach.
Diving at Phuket is cattle boats and long drives to the sites, and you will only go the the relatively few sites where and when they have scheduled; forget sunrise or night dives. Malapascua is small boat diving, often one can ask to go to a particular site and if you want 4 or maybe 5 five dives a day it can be done.
Phuket has some nice sites (I like Shark Point the best, but Anemone Reef is also beautiful) but not too many; the cattle boats have a very limited site selection. Actually if going to Phuket maybe better to then take a boat to Phi Phi Island where there is more site variety and shorter rides. Or take a liveaboard to the Similan islands which I have not seen but is supposed to be great.
Malapascua has in my opinion a better variety of sites. Monad Shoal (about a 30 minute ride) is the best known and is great when the thresher sharks or mantas show, but otherwise you spend 50 minutes watching plankton drift by...figure on average to have a shark sighting only every 2-3 dives. Gato Island is great, good swim-thru that really doesn't require cave cert and probably will see whitetips sharks afterwards. Going to Calangaman Island for a day trip offers two great wall dives and a good beach BBQ. Most of the local sites are also good and less than a 15 minute dive.
At Malapascua I can strongly recommend Thresher Shark Divers. At Phuket no particular shop recommendation but I did an AOW course years ago with Marcia Fisk Ong (
http://gekkoscubadivers.com/) and she was very good for a course and a source of info.
Malapascua is much less expensive.
My vote would definitely be Malapascua, but you'll have fun either place. Enjoy!