Try 'em both.

Run alternating careers in different boats or flotillas. Right now I've been experimenting with that. I have a career in the Med with a VIIC and when I die or get pulled from sea duty, I resume a career in the Atlantic with a IXC. When I die or get pulled from sea duty in the Atlantic I go back to the Med.
I've read on these forums where people have different careers in each of the different flotillas and rotate through them.
At first, I couldn't wait till I could upgrade from a type VIIB to a IXB later in the war. When my career was ended due to realistic career lengths in SH3Commander, I started a new career in late '41 with a IXB. Of course, with the IX came patrols in distant lands-Freetown and off the coast of the US once they entered the conflict.
Initially, I loved patrolling off the US coast and in the Carribean(lots of lone tankers and plenty of sunshine and boat drinks

) in a sub with a lot of torpedoes

.
After a couple of patrols like that though, I found myself missing my type VII. Some of those long patrols can get pretty boring and I thought I needed a change.
After taking a 3-4 month break from SH3, I started up a new career in the Med with a VIIC, which I have enjoyed. After getting sunk there, I resumed my Atlantic career in the IX. I recently lost that sub on the way to Freetown and have started a new career in the Med with the VII.
I'll probably continue alternating like that for a while and see how that goes.
My ultimate goal though is to experience the entire war. I play DiD but when I die or get pulled from sea duty, I start a new career from where the last one left off. The alternating flotillas is just a way to spice things up for a change.
I'm currently in Sept. '43 in the Med(just moved to Toulon) and it is April '43 in the Atlantic out of Lorient(looking forward to the spring sunshine while crossing the Bay of Biscay in May

).