In 1940, fighting and winning the 'Battle of Britain' knocks the UK out of the war, if Sea Lion follows that up. Conquering Malta in 1940 leaves the UK in the war, with armaments factories getting up to speed, no 'invasion scare' to screw up UK tank production and a 'Hitler didn't even make the preliminary moves necessary attempt to invade us' propaganda victory.
In 1942 with the USA in the war Germany is on a clock, as the USA arms up and trains up. Taking Malta is a 'so what?' moment, where Germany has just spent several months with the clock running clearing an obstacle to its logistics chain. Taking Egypt in 1942 (if Rommel can pull that off, with cooperation from the senior British commanders in the region messing up yet again) destabilises the UK government (Churchill already was hauled over the coals over the fall of Singapore and the loss of Tobruk - he may not survive a third vote) and decisively shuts the Suez Canal, besides potentially threatening Russia from the SW (Okay: it's nasty terrain, but it's yet another thing for the Russians to worry about, as the Battle of Stalingrad rages and hangs in the balance.) Egypt is a big 'all in' move, and - with the USA in the war - the kind of move which Germany increasingly needs to pull off (and which it certainly won't, if it doesn't try them.)