I cannot see a reason why the Germans would change OTL Barbarossa and focus on a drive to Baku. First and foremost, the Germans didn't plan for a multi-year campaign so as to focus on a drive to Caucasus. If the OKW expect the war will take only a few months, why bother? They would have to change
completely their strategic thinking and instead of a knock-out blow (as in OTL) they would need to plan for at least a two year campaign season where in Year 1 they capture Baku and in Year 2 they drive to Moscow and knock the USSR out of the war.
Moreover, even the most insanely optimistic Heer staff officer cannot hope to reach Baku before winter. Reaching Baku from Donbas as in Fall Blau is one thing. Reaching Baku from Prut is insane even for the most insane German officer.
Overall, I sincerely doubt there will be any major difference in Barbarossa.
Crete as a heavy bomber base comes up so many times I've bookmarked my previous thoughts on it, which you can find
here. TLDR- requires huge investment that will not be forthcoming unless and until the US decide they want to base heavy bombers there, the British cannot afford to invest so much in an area that they will not see usage of post-war.
I think it depends. If the British offer Cyprus to Greece while retaining bases there, in order to secure Souda and an adjacent airbase complex, then the Greeks would jump at the opportunity. Moreover, in TTL the Greeks will be viewed as a more reliable and valuable ally.
The Foreign Office has to decide how british interests would be better served: have bases in both Crete and Cyprus or just keep Cyprus as a colony. Frankly, Britain had extremely few economic interests in Cyprus. The island's importance laid on its strategic location and being an unsinkable carrier for the RAF. What I propose is a win-win: Britain strengthens its power projection in the Mediterranean via Crete, while keeping what is valuable in Cyprus. At the same time, Albion gains good will with Greece. In such case, Britain doesn't lose its influence in Greece as it did in post-1946. While USA will be the western hegemon of the post-war era, Britain can claim to be the second-best more important regional hegemon.
If the resources are found, Souda can be turned into a great port and a secondary smaller one can be built in Tympaki at the south coast. If the Luftwaffe is blasting cretan ports, the extra miles to the north do not make a great difference to be honest. Due to distances involved (and the Luftwaffe operating from mainland Greece with worse logistics compared to Sicily) it will be way easier for the Allies compared to Malta. After all, Crete can feed itself. Not to mention that ina few months the RAF will oeprate fighters from the island to act as a shield for the convoys.
Why do I say that the RAF can operate fighters soonish? Because if the Luftwaffe could stage a significant part of X. Fliegerkorps in Crete in a matter of months, why the British cannot do such thing? After all, the OTL german logistics in the Aegrean were atrocious, having to rely on a handful of transports and were partially depended on wooden fishing boats.
Naturally, bombers are a whole different thing. But by late 1941 the RAF can have a decent fighter presence in the island along with a squadron of Stringbags.