I managed to visit 4 of the 6 inscribed temples so I wanted to leave some short thoughts on them (and also some updated pricing info)! You can buy a pass to all museum sites in Malta (besides the Hypogeum) for 60 euros now as of 2025... but this is too expensive if you just want to see the WHS. So, instead I spent 26 euro seeing 4 temples.
Tarxien: only a 10 min walk from the Hypogeum! Tarxien has rock carvings, something I didn't see at the other 4 temples -- giving it a different "vibe" from the others. Hypogeum museum staff even gave me a map at the specifically encouraging me to visit it so it's hard to pass up :) I think this is also the only site I visited that is completely wheelchair accessible, with paved ramps taking you in and around the temple.
Cons: most of what was interesting there seemed to be reconstructions. Tarxien also doesn't stand as tall as the other sites.
Ħaġar Qim & Mnajdra: These two are really similar and hard for me to differentiate. Main benefit is that they aren't hard to get to from Valleta and are near touristy things like the Blue Grotto. They are a 10 minute walk away from one another, so it makes sense to visit both.
You can buy a combo ticket for the 3 aforementioned temples (Tarxien, Ħaġar Qim & Mnajdra) for 16 euros.
Ġgantija (pictured): Located on Gozo -- which made it a much longer trip comparatively. It's nice but I didn't feel like it was particularly different from Ħaġar Qim & Mnajdra as a visitor. Main benefit for me was the lack of crowded tour groups.
Cost = 10 euros.
I can't choose favorites! Each of the three locations had different pros and cons. However, if you can only visit one location, I would say visit the combined site of Ħaġar Qim & Mnajdra :) Easy enough to get to, offers 2 temples, has a museum attached, and gives you the giant Ġgantija "feel" without needing to trek to Gozo for a day.