The biggest problem the Germans would have faced in Sealion historically wasn't landing the troops: it was keeping them supplied afterwards. The initial landing would have the benefit of surprise; but after that, British torpedo boats and destroyers and submarines and aircraft would have been patrolling the seas off the beachhead sinking every transport that tried to get through. After a couple of weeks the starving German troops would probably have been forced to surrender. Trouble is, it doesn't work that way in HoI3 because disrupting a supply convoy is really hard. The game tries to use the same mechanics to represent U-boats hunting convoys in the vastness of the entire Atlantic Ocean, and MTBs sinking transport barges that are heading to a specific, known place in coastal waters at fixed times.
How to fix it? Well, a couple of suggestions, based on the idea that this DLC doesn't need to be balanced for all nations :
1. You're already using modifiers to the AI's convoy defence chances. Why not give Britain a specific triggered modifer that gives them a huge bonus to their convoy attack efficiency, triggered only if Axis units occupy at least one but less than all provinces in the British Isles?
2. Alternatively, how about creating a special AI-only "coastal defence" unit to represent MTBs, coastal defence ships, and even minefields? It would be similar to a submarine in that it would be very good against convoys, low visibility against enemy detection, but not especially effective against surface ships - and give it a very short range, basically only into the sea zone adjacent to the port it was based in. Give the UK and perhaps a few other countries a bunch of them at the start of the game.