Love 'em both, but I play GWX mostly (about 70% SH3, 30% SH4.) I'd be happy bouncing back and forth about 50/50 but SH4 taxes my system to much that even at high TC ratios, it takes forever to get anywhere.
I haven't modded SH4 because, as is, my system struggles with it and I don't want to hurt my baby any more than I have.
If you have the specs, though, it's a tough call to make. Depends on my mood, personally. SH4 is much more optimistic, and you can really put a hurtin' on some convoys with 10 fish at your call at once. SH3 really makes you feel desperate, and this only gets worse as the war goes on. You get 5 or 6 shots, then hope the Brits don't DC you to the bottom. And, you know you'll lose anyway, so you know it's a losing fight. Great atmosphere in both cases, just different flavors.
You'd have fun either way.
$0.02
-Zilch