SH2, SH3 and SH4 (SH1 for that matter too) are much alike in terms of learning curves, although the current glitches in SH4 may lead to frustration for someone getting the hang of things, so I would go for SH3 patched up (official patches).
For SH3, there is of course the ubiquitous GWX (Grey Wolves) free super-mod add-on, which makes SH3 a much better game/sim, although it might make things a bit tough if you want to play on full realism and are not used to the tactics required (GWX is also a big five-part download, which could take a while if you haven't got a good broadband connection).
SH2 is also pretty good - it certainly has a bigger manual than the current SH4, being 115 pages, as opposed to the paltry 60-page effort that comes with SH4. But you might find the SH2 graphics a bit off-putting when you realise what later SH versions add on the eye-candy front, although it's certainly not dreadful.
Most hard-core virtual sub skippers are less concerned about the graphics anyway, since they are usually unable to see most of them on full realism settings, but when you're starting out, they help a lot as you can see exactly where your torpedoes go if they miss etc, and this helps in learning where you might have gone wrong. Easier settings with the external camera view enabled also make avoiding being depth-charged by a destroyer a simpler affair.
German sub sims (i.e. SH2 and 3) offer more in terms of variety than US ones (SH1 and 4), as there is a far more varied assortment of equipment available and a wider variety of submarines, so a lengthy career as a German Sub commander tends to offer a pleasingly progressive introduction to things like radar, and more complex types of torpedo.
Having said that, SH4 (despite its current faults awaiting a patch) has a far wider variety of mission types than any previous version of SH. So if SH4 runs okay on your machine and you want to use simple settings for targetting and the like and not be confused by all the German stuff, then SH4 is certainly the prettiest option for a beginner.
Don't worry about being new to sub sims either, everyone on this forum was new to sub sims at some point, and most people will gladly help you out with any problems you might have. Anything looks complicated if you've never tried it before, so stick at it, and good hunting!
Chock
