I seem to remember that Deep Blue were going to do some diving around Croatia using the Loyal Watcher (or maybe I dreamt it!).
I've dived out of Dubrovnik and somewhere further to the North (name escapes me on a Friday afternoon) and the diving was ok, nothing too splendid and not too much fish-life, but reasonably warm clear water and beautiful coast-lines.
A lot of flights go via Zagreb but you can get direct flights to Split and Dubrovnik, and as someone else has commented Neilson do diving holidays to one of the islands.
Hi, Dived Croatia a couple of years back, we were based on the isle of Brac (pro bratch) sea temerature were early 20's in June, fab un adulterated diving, Go for it. I can't help you on dive org's I was diving with the services.