You need to look at Dunkirk again. The German airpower was able to do what against slow clumsy transport ships you said?
Dunkirk is an unfair example of the Luftwaffe's anti-naval abilities. Halder complains of bad weather grounding it often during the Dunkirk evacuation [source: pp 808 The Rise and Fall of the Third Reich, vol 2] and the other "half of the time" the Luftwaffe was "Unexpectedly opposed by the RAF based across the Channel and successfully challenged for the first time of the war". That is not quite the same as "Leaving the ships to the wolves" as Herr Oberst said you cannot do (without repercussion).
The Luftwaffe still knocked out 243 of 861 shipping vessels - let's call that a fourth - in a few days with bad weather and the RAF winning the first aerial battles of the war for the allies. [All in the Rise and Fall of the Third Reich, same pages]
The German High Command was rather stunned, and prior to this example had factored very little of the RAF's capacities. During the Battle over Britain the British wouldn't enjoy the complete surprise of the spitfire's effectiveness again, although effective Radar facilities also would shock the Germans.
Given the context of "What if sealion..." I'd assert that the Luftwaffe saw "Fair weather" and had beaten (or at least driven back) the RAF in the skies over Britain/English Channel. I think that the most valid argument against a successful sealion is that the UK was outproducing Germany in Aircraft production pretty handily in 1941, making air supremacy hard to attain for the Germans. (Overlooking the Historical failures, of course)
Manstein writes (and I'm inclined to agree) that the outcome of the decisive battle in the English Channel would have sealed the fate of the invading forces - but that the conditions would be much more favorable for the Germans fighting the British over the channel rather than over mainland Britain. Where British pilots could return to fighter base and get back into the fight after a plane was shot down. (Sorry my copy of Lost Victories is on loan, I can't give a page)
With regards to the Soviet Union attacking Germany in the rear, I doubt it for a few reasons:
Firstly, the Optimal time would have been while Germany was attacking France, Britian, Belgium and the Netherlands, not after Germany had overran them and forced the British back the home islands. What is not in contention is if the German Fleets/Airforce could have shipped (and supplied) much more than a tithe of the German Army to Britain. The rest of that army would have been prepared for a defensive war against the Soviets, save a few reserves.
Secondly, the German Ambassador to Moscow (Schulenburg) had stated in May of 1941, "...Stalin has set himself the goal of preserving the Soviet Union from a conflict with Germany." [pp 924 The Rise and Fall of the Third Reich] Or in other words Russia does not want war with Germany. Granted, he's one person, and a person can make a mistake. However, he had something none of us here have - Access to Stalin and Molotov, giving him a little more credibility.
