It's kind of weird that a small island nation like Malta hosts two great prehistoric sites. But it does, with the Hypogeum being the most stunning. The temples are also great and they offer the added benefit of taking you all across the islands of Malta.
Of the temples I have seen Ħaġar Qim and Mnajdra were the most scenic; the previous reviewers seem to indicate the same. Built on a cliff, you get great views of the Mediterranean Sea and Filfla island. Nowadays, both temples are covered by huge tent constructions for protective reasons. Our resident Maltese, Clyde, disparaged the constructions. While I understand the necessity, I have to agree with Clyde: The tents really take away from the atmosphere. The light just isn't the same
Also tent covered is Tarxien. It's a fairly large site and it's also not as old as the others. To me, it offered the best visitor experience as there are pathways and signs. There is even some rock-art. If you visit only one temple, Tarxien is a good choice. It's also a good choice if you are time limited as it's the closest to Valletta and a few blocks down the road from the Hypogeum. Indeed, with proper planning (and a reservation for the Hypogeum) you could cover all Maltese sites in a single day.
Skorba and Ta'Hagrat are without a tent cover. Both a rather small. For Skorba, you can skip buying a ticket as you can see everything through the fence. The same is more or less true of Ta'Hagrat.
Due to time reasons, I had to skip Gozo. I think you need a full day to make that visit worthwhile. And I am a bit sad that I did not find the time to go.
Getting There
There are direct buses to all sites on Malta island from Valletta and google maps has the connections. The only minor challenge is to travel between the southern temples (Ħaġar Qim & Mnajdra Qrendi) and the western ones (Skorba & Ta' Hagrat), but it's possible, too.
In my case, I took a morning bus from Valletta to Ħaġar Qim and Mnajdra. After my visit, I took another bus to the Coastal Cliffs (T), from where I hiked to Mdina (T) with a short stop at the St Paul's Catacombs (T). And as I was in a hiking mood, I continued to Ta' Hagrat. I am also pretty sure that I passed through the Victoria Lines (T) along the way. Word of advice, though: Malta is not a hiking place. It's a pity, but most of the time I had to walk along the road.
Tarxien I combined with the Hypogeum the next day.
Practicalities
Having to buy a ticket at each site felt cumbersome. There is no combined ticket for all temples. But there is a Multipass covering most of the Malta heritage sites (i.e. everything but Hypogeum). It is expensive, though, coming in at 50€.