A Microcosm of the Mediterranean
Malta would make a very good destination for your honeymoon, particularly if you are interested in history, architecture, scuba diving, and even some easy hiking. A honeymoon in Malta is not known to be the ultimate beach destination as a lot of the beaches are rocky rather than sandy. But the rocky bays can be stunning if you find yourselves alone there around sunset. The history in Malta is particularly interesting too, and Valetta is just wonderful.
Gozo some very nice sandy beaches and is also likely to be more quiet and peaceful. But the public transport system in Gozo is not always great.
Malta, on the other hand, has a very good bus system, so you can hike everywhere and catch a bus back to Valetta, which can in itself be a delightful experience. Honeymooning in both Malta and Gozo is probably the best solution, so you will be able to enjoy the best of both worlds.