If your looking to just improve the hull specs - try titanium boats instead. I havent updated it to include more than gato and balao like I did with nuke boat - but I will this weekend when I have time to spare. (Work during the week so my evenings are game time - not mod time
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There is some minor depth fluctuations in Nuke Boat - its unavoidable at high speed although I tweaked the MBT flooding time so that its usually no more than about 10 feet on a hard dive before ya even back out. If your headed toward the bottom in shallow water - you simply have to catch your depth faster (setting it shallower than the bottom) than you would have to with no mod. Its all a matter of how you want to play. Realistically - a sub at high speed never just hit "perfect depth" - you have planesman and a diving officer constantly correcting for minor imbalances.
Killersub is designed with a different purpose in mind than Nuke Boats. Comparing them really isnt effective as its like apples and oranges. Killersub changed speed some - but its main change was weapon related. I dont think Killersub changed fuel consumption or battery range. Nuke Boats makes no changes to weapons at all from the stock game, but focuses only on boat performance and near invulnerability (hull wise).
Comparing the two is like comparing RFB and Trigger Maru = both of these mods do what they aimed for - but the goal is different.
Hope this helps!