For more realism i think of two solutions:
-You should fire 2 or 3 torpedoes for valuable ships like tankers or big freighters over 6.000 tons to ensure success.
-Someone should lower the tonnage of each ship because it's way too high in SH3 vs RL ( just look at uboat.net : ships sunk over 6.000 tons are not so often and sometimes they are only damaged)

Unfortunately just lowering the tonnage of each ship in the game would also be unrealistic. The Liberty ships really were registered at 7176-7255 tons. The T2 tanker really was 10,500 tons. The problem is having so many appear in the game. Fixing it is a real job.

There are maybe too many high ton ships, though looking at the top ace's stats from his type VIIb missions he had a lot of high ton ships. His last patrol was 70k+ tons and he had several 10k ton or higher ships in that one. In his last 5 missions almost all the ships were 5,000 tons or higher. Of course he isn't the norm, because he was the top ace and these missions were in 1940, when tonnage totals were at there highest. I may have to see if I can figure out the average ship tonnage would have been.

The tonnage per ship for typeIIA's is quite small. There range prevented them from getting patrols along the Western side of the UK or the Atlantic. Lots more coastel vessels and trawlers.

I think the biggest problems with excess tonnage in game occur early on in 1939, when its just too easy to rack up 40 tons or higher on helpless merchants in a typeVIIB. This is where its also noticeable that you come across a lot of 6K to 10K single ships. I find that I can't let them go though, doesn't seem realistic either to say will its too big I won't sink her. I get around this whole situation by starting with a typeIIA for 6 to 8 missions.

That uboat.net site is amazing. They have all the u-boat attacks analyzed. So just doing simple math with the numbers there gives an average tonnage of 4,875.9 per ship sunk. A higher number than I realized.

I do a few things to handicap myself.Firstly I have to spend two weeks in my assigned patrol grid, after that I can patrol all of the adjacent squares, so 9 in total.The problem with radio contacts is that the ships are far too easily intercepted.In real life ships would change course more often and the radio reports wouldn't be so accurate in the first place.To simulate this I ignore 3/4 of interceptable contacts.I do this radomly by tossing a coin twice.Visual contacts I ignore 1/2 the time including convoys.If I get a hydrophone contact I ignore it untill it becomes visable although I do watch the horizon for it, just not altering speed or course.I have to attack on the surface at night and I can't attack if the wind speed is 15m/s.Opportunities to sink capital ships are far too common so again I ignore 3/4 of them.I don't allow myself to target destroyers at all.I do use the deck gun but only in a flat calm and it's not nearly such a powerful weopen in gwx anyway.
The combination of all this slows me down quite a bit but makes the ships I do sink that much more memorable.