We have just come back from Malta (last week), my 2 daughters are 1 and 2.
Have to say that I was dissapointed with Malta, very few beaches, they were nice but were just so packed and a lot of them you had to go down steep steps so a no no with a buggy. It was also far far to hot, 37 degrees, OK, I know it was July but we were going with MIL, so didnt have much choice of when to go.
The waterpark is closed at the moment, daft considering it is their peak season, they have a marine park where you can swim with dolphins, which is expensive and not really worth it according to friends.
There is the Popeye Village, where they filmed the popeye film and they have turned it into an attraction for kids. Well, half of it was closed (again, Peak Season?????) and we couldnt get into the restaurant and a lot of the village with a buggy.
Last year we went to Sardinia, again not much in the way of amusements for children, but gorgeous deserted beaches.
In my opinion I dont think that Malta is ideal for a family holiday with children.