ORIGINAL: Feltan
WRT the sub game.
Early on take special care to deploy Dutch subs and the S boats -- in '42 they will be the kill leaders if you use them wisely. With dud torpedoes, deployment of fleet boats is up for debate. You can deploy them on the approaches to the Japanese homeland via Pearl, or eventually Midway and just ignore the fact that a lot (hmm... maybe 75%) of the hits will be duds. I often use them for emergency supply runs to Singers and Bataan to try and prolong things a tad more, but just a tad.
Set up your key sub bases and if they don't have a shipyard use AR/ARD at them to repair light damage. At first the AS situation isn't too good, but later you will get so many of them that they will be begging for work.
Regards,
Feltan
Somebody posted up data from their game a couple of weeks ago that showed fleet boats really aren't that bad. Maybe in December of '41, but in '42 they do pretty well. Mostly due to their superior range, durability, and ammo stocks. As you say, their torpedoes may fail more but they also shoot more torpedoes over the course of a patrol. And once Japan has taken all of the SRA, they're really the only viable option to interdict shipping around the Home Islands.
I would recommend deploying all boats to the best of your ability. I've found subs to be an incredible asset in this game, for both sides. They can take out any ship, at any time, and you get a lot of them. My favorite spots for portions of my deployment are from Townsville or somewhere in the Solomons (easy access to CentPac and slightly closer to Japan than Hawaii is), with Brisbane/Sydney available for repairs. Especially if you can get the support ships (AS, AR) out of the DEI and to the eastern coast of Australia.