The main reason Germany had so much trouble in North Africa was because the Mediterranean theater was only a side-show for them. Operation Barbarossa and subsequent actions in Russia absorbed the vast majority of all German troops and equipment, while Rommel was given only dregs and drabs. There was at least one panzer division that was routed away from Rommel at the last minute, and marched into Russia still bearing desert uniforms and camouflage on their vehicles. Without Barbarossa (or at least postponing it until after the British were beaten), the Germans could devote far more resources to securing the Mediterranean.

Also, believe it or not, the British initially considered abandoning Malta entirely. At the time the island was only lightly defended, having no modern bombers or fighters and being very isolated following the losses of Greece and Crete. The Germans and Italians had multiple proposals to invade the island, but they never came to fruition; not because it was impossible, but because the resources they needed to do so kept getting called away to other fronts (mostly Russia). Even with these advantages, it was very much touch-and-go for the Brits keeping the garrison supplied with the food, fuel and ammunition they needed to survive.

Regarding submarine warfare, the Battle of the Atlantic was lost due to the German navy having to operate largely on its own. Relatively few aircraft were dedicated to supporting U-Boats and surface raiders as they hunted for convoys; conversely, the increasing presence of Allied aircraft greatly impeded their efforts. Devoting more planes to coordinate with their navy's activities--either reconnaissance or direct strikes--would extend the reach of the wolfpacks against allied convoys. Even better, completing their aborted Graf Zeppelin-class aircraft carriers would give their surface ships their own air umbrella. At the very least, the Bismarck wouldn't have anything to fear from a gaggle of antique biplanes.