Staying at Jonathans place was exactly what we needed. We made the place our headquarters for exploring Malta (and Gozo). Once you understand the maze of tunnels right in front of the house that leads to all the Bus stops, you literally need 5 minutes to hop on to any location. Make sure to get the "explorer" bus cards with 7 days unlimited travel for ~20€.
Jonathan was always available via WhatsApp if we had a quick question, e.g. what he would recommend visiting in Gozo ;). The appartement has all the things you need - including big freezer and fridge! There are several minimarkets in walking distance and a Lidl about 30 minutes away.
If you come to Malta in Summer expect it to be hot. Really hot. We needed about 3 days to adjust to the heat, especially at night, but afterwards it was fine. I can only recommend Jonathan and his appartement. Go book it, now! :)