Crete would be under the same threat of aerial attack as Malta, and Britain needed its Spitfires for pointless and wasteful Continental rhubarbs. As the usefulness of Malta could be, and was suppressed with heavy effort, so could Crete, and both could be only defended and operationally effective with heavy defensive effort. Malta only got Spitfires after they had lost their edge over France, to Focke-Wulfs. Do you get twice the value of Malta, with twice the effort of maintaining Crete as well? I don't think so. In favor of maintaining Crete, it would have saved thousands of Cretans who were executed. Another plus is that it would require a concerted effort by the Luftwaffe to suppress, at a time when they had other tasks at hand. On the debit side, it would have encouraged Churchill to dabble in Dodecanese adventures, to everyone's cost.
I'm not so sure... the strategic bombing
potential of Crete (not the actual value) IMO would be a major draw for RAF resources and, most likely Luftwaffe resources. Furthermore, maintaining Crete would have been vital to maintaining the legitimacy of the Greek government as well as a staging area for further Aegean adventures/Churchill's obsession with the supposed "Soft Underbelly of Europe". IMO Churchill pries the Spitfires from Fighter Command and sends them to the Mediterranean to keep Crete in allied hands.
Operation Battleaxe likely gets postponed in order to reinforce Crete, which might not be a bad thing for the Allies, considering that it was rushed in OTL. Rommel's logistics are also likely worse than OTL.
Though the UK will need to now send convoys to Crete, sending convoys to Malta will be much easier without LW bases in Crete. Furthermore, there wouldn't be any need for the "Club Runs" in TTL if my math is right. The RAF could easily reinforce Malta by staging Hurricanes and later Spitfires through Maleme airfield.
Crete holding also has MAJOR implications for Greek history as the Greek government in TTL will have exponentially greater legitimacy. With the prospect of an Allied invasion right around the corner, traditional Greek elites likely opt not to collaborate with the German/Italian governments and instead encourage resistance. This in turn likely butterflies away the development of ELAS. Furthermore it likely makes life much worse for the Italians and Germans in TTL, perhaps the Germans take a more active role in the Italian zone in TTL to ensure it's security? If the Germans take it upon themselves to occupy more of the islands Churchill might be dissuaded.
Anyhow, I'd wager that the strain of holding Crete forces Britain to act more conservatively in North Africa in 1941 and early 1942 while sucking up more Luftwaffe resources than OTL. Perhaps in TTL, they decide to adopt a defensive strategy and dig in at El Alamein in order to free up resources for Crete?
America's entry into the war releases more shipping which allows Crete to finally reach it's full potential as a strategic bombing base. By Q1 1943 at the earliest (probably more like Q2) Ploesti and other Balkan targets come under sustained attack from Allied aircraft. This in turn could aid the allied invasion of Italy as Hitler may very well send more reinforcements to Army Group E than OTL.