I get your point. A realistic Med campaign would be very boring from a u-boat view. Until the Torch landings there was very little traffic to shoot at. Lots of small sailing vessels near Egypt and Palestine, ASW groups near Gibraltar and very rare fleet operations and heavily escorted convoys. Not many allied lone merchants!
https://uboat.net/ops/med-ove.htm
Malta is a strange one as the air cover varied greatly depending on how hard the Germans (and Italians) were trying to bomb the place. However there was always some allied presence. Operating a uboat thereabouts would be very difficult because of the huge amounts of mines spread by both sides. Mines do not really provide satisfying game play.
There really should be some areas where operating on the surface in good weather is extremely dangerous. Gibraltar should be one of these. The air cover needs to be high enough to force the player to only surface for the minimum time necessary. As I understand the game this would have to be tweaked with scripted patrols. Apart from the work involved the trouble with these is I don't think they account for weather conditions. The other big problem for a Med campaign is the lousy SH3 weather - it does NOT feel right!