My favourite site was the hypogeum, it's a UNESCO world heritage site and it is amazing, but tickets may already be sold out for Feb half-term, as they only let about 12 people in every hour (AI actually says 8 people, they have may have reduced capacity since we went). We stayed in Valletta itself, at a very small hotel called Paulos Valetta. Location is great, I really liked being in the middle of Valetta, easy access to the sites and the rest of the island. I bought a family heritage Malta pass which covered most government owned sites on Gozo and Malta, we had 10 days in Malta, this may not be a cost effective option though for a 4 day stay, need to add up all the entry fees and work that out. We spent 1.5 days in Valetta, did the war rooms, grand masters palace, and an underground Valetta tour, amongst other bits and pieces and otherwise used it as a base and took day-trips, so Hagar Qim and Blue Grotto one day, another day we did Uber from Valletta to the Hypogeum (not covered by the pass), totally fabulous, then walked to the Tarxien temples (was covered by the pass) and then Uber to the 3 cities and used the pass for the Inquisitors Palace and Fort Saint Angelo, then ferry back to Valletta. Mdina is another great day trip, there is the walled city (lots of Instagram spots) but also Roman House with good mosaics just outside the walled city and the catacombs in nearby Rabat (10 minutes walk from the walled city). Recommend eating cake in the fontanella tea rooms in the walled city of Mdina, so many cake options!. There are at least a few sites in Valetta not covered by the pass, like the cathedral, war rooms, Casa Rico Piccola. I have very fond memories of our holiday, really enjoyed it.