There's lots of room for improvement in even modded SH3 but I don't consider it a "poor simulation", though without the excellent work done by the various modders it definitely is.
The escorts/aircraft are weak, etc. but whatever. The very weak damage model is what needs the most improvement to me.
Some user imposed rules if one desires can help a little; i.e. since chlorine leaks aren't modeled, if the batteries are destroyed or more than thirty (arbitrary number I picked) minutes repair time, I surface and surrender even though one wouldn't have to in the game.
The problem with user imposed rules is trying to remember them in the heat of action !