I went to Malta last october and talked to as many schools as I could.
The first was fun and adventure/diveshack, liked the guy but they didn't convince me as a serious dive operation.
After that I talked to people at Dive deep blue, subway, Strand and Maltaqua. All of which seemed really good people, well equiped, helpful and professional. I could have gone with any of them, they all seemed great.
I ended up going with Maltaqua and wasn't disappointed (there is a trip report from me around here somewhere).
Just about all the operations work on a collection basis, so where you are in relation to the dive centre becomes the dive centres problem. Most schools dive all round the island anyway and so it doesn't really matter that much.
They will arrange the medical, only one was needed for me to do my AOW and then to contiinue to dive in Malta, it takes about 2 or 3 minutes per person. Get a copy of the standard questionnaire that most places use and give it to the group, if any of them have to say yes to any of the questions then it would be better to see a doctor at home.
One of the main questions is which language you want to train in. All people will offer training in multiple langauages, always English, normally German and or French and sometimes other languages (depending on the size of the school, some will only have 1 instructor others will have 5 or 10). If you are coming with a group of students that would prefer to learn in Dutch then it would be good if you choose a centre that has more than one instructor fluent in that language, just in case. Also make sure they have enough books in the language you wish to use.
As an example my gf is french and Maltaqua's french instructor had a cold and couldn't dive, so he done the classroom lessons in French and then another instructor done the water work in English (well sign language really).
Just a few things to bear in mind.
BTW I forgot to mention, you'll have a great time, its agreat place
Conor