I might suggest taking a look around at the current crop of new subs. There are some very interesting subs, with bombers and scouts. Also some big deck guns on the MN and UK might be fun. The KM has some advantages and several have 6 or more front tubes.
The grind through SS1 and SS2 is more difficult with the introduction of higher tier subs, but they're still fun.
If you want best, best, best. Then you need to know exactly what the developers have in mind for the not-yet-released SS6 that you would then need to be going for. Otherwise, any sub line is good, just bring up a parallel BB line so that you can nurture your support sailors, as your gunners will be doing little until higher levels and need something to shoot.
All of the SS1 are about equal - slow and pathetic. All of the SS2 are about equal, with the KM having advantage with P-Torps. SS3 is much improved and all are good at destroying enemy. Better systems. SS4s are little better and the KM has the U-flak guns. IJN is a BB hurtin machine with 8 fronts. UK is an underwater tank. MN is a small, agile torp spittin terror. SS5 is a change of pace; KM falls back to basic deck gun (useless), but improves in some areas. US Gato is new SS5 wunderkind with 6+4 tube setup.
So to answer your question, what SS do you want to waste all your time to achieve...???
There isn't a biggest/baddest SS. They all get clobbered by BBs, rained on with HH, and killed by other SS.
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