One issue with garrison sizes is that Malta is less than one twentieth the size of Crete, and much more developed. Malta is a defender's paradise and an attacker's nightmare, so you'd either have to flatten the place, or starve it out, and the latter isn't practical, as the resources you'd need wouldn't be available.Crete was the costliest naval engagement for the RN in the entire war. They lost 4 cruisers and 6 destroyers and had one AC, 2 BBs, and 4 cruisers put out of action for a long time, Maybe the time to hit Malta was right after Crete. The relative strength of the RM v. the RN was at its highest.
Also Crete was much closer to British bases and further from Axis airfields and ports. The garrison on Crete was about twice the size of the garrison on Malta. There was some British air power on Crete at the beginning of the battle and more could be brought in with direct flights rather than having to use ACs. The Italian navy was not really present for the Crete operation. All of these things make Crete a much, much more attractive venue for the RN in comparison with Malta.