RUB is a very good start point. its put toguether a lot of stand alone mods in one pack and don´t cause problems.
For the deck gun reload times, map manual plotting, dark water, exist some mods that put things like the default game.
I have a personal modification of Rub with the things that i don´t like removed, and other mods (dials,screens, ...)
Despite this, the last rub 1.44 have a improved manual plotting that is better of the previous version.
one day i have to try do hardcore manual plotting....
Another good option is Iub, but i don´t have this mod yet.