I'm using SH3 and SH4. SH3 with the GWX mod and SH4 with only one or two tweeks of my own (pretty much standard SH4 though, as I'm waiting to see what befalls us when the next patch comes out, if it does).
I don't think the comparison is lame at all, as all you are really doing is comparing the tactics of a fleet boat versus one which was typically meant for a short duration coastal patrol, but both of which ended up being used outside of their original intended purpose.
Most military vehicles end up having their role altered or changed when they are in service for a long time and the ability of a machine to cope with having to take on differing tactical roles is one of the things that determines how good and versatile a platform it is. The B-17 Flying Fortress was originally conceived as a maritime patrol bomber for example, which is not the role it became famous in.
Also, as people have noted, there is the switch you have to make on keyboard assignments. Fortunately for me, I'm used to doing that, as I spend all day training people in applications on Apple Macs, and then come home and start using a PC. So if you think keyboard assignment differences are confusing, try constantly having your alt key's position moved and effectively having two different control keys!
Although I was initially a little puzzled about why the keyboard assignments were altered on what is effectively a souped-up SH3 in a different theatre of war, I can see a kind of fuzzy logic about it: It conveys the notion that you are in a boat designed by a different nation with dissimilar appoaches to how stuff worked or was implemented.
Oddly enough, one of the worst submarine films of all time (U-571) is the only movie that's ever really addressed this, when the US crew are briefly puzzled about where all the controls are in a sub unfamiliar to them. However, they do seem to manage to work it out rather quickly in a manner more befitting an episode of the A-Team rather than a serious sub movie (I half expected the Dah-de dah dah! A-Team music to kick in when I was watching that part of U-571
)
Got to love having more tubes and more speed on the Yank subs, but I do find myself wishing for the speed and manueverability of the Jerry stuff.
It's also interesting to note the changes that are highlighted over the period of several years of development. Nobody could fail to miss the massive advances the Germans managed with regard to sub design and equipment in comparison to the almost plodding progress of US development. It sometimes makes you wonder how the Germans actually managed to lose the war, when they had all those great ideas such as the Type 21 sub, hydraulic loading, acoustic and pattern running torpedoes, jet fighters, cruise missiles, guided ballistic missiles, stealth technology, superguns, assault rifles etc etc.