First, WELCOME ABOARD!
The only reason SH4 got the "good" graphics is that it's two years newer. While I love them all, I agree with Torplexed that the Pacific War has gotten short shrift of late. I would like to see SH3 brought up to current standards, but I'll play both until something better comes along, which I may not be around to see. And, still agreeing, I would say that after three years the German version is still getting better every day, with new immersion mods constantly adding to the feel. There are two great GUI mods making manual targetting much more realistic, and I'm rather impatiently waiting for part two of the 'Kiel Canal Locks' mod, so I can waste even more time just watching the scenery.
As for what and how to play, these sims are now so advanced that you can have fun doing anything you like, from good old-fashioned 'just going and killing something' to having to use manual navigation, including taking sun-sightings with the sextant.
Please, ask all the questions you like. But not right now - this has me so excited I have to go play.