I have both games and I prefer playing SH4 (with the Real Fleet Boat and Run Silent, Run Deep mods). Here are a few reasons:
- The graphics in SH4 are very good, especially the environmental stuff, like sea and sky. It does take a stronger computer to run at full graphic detail than SHIII, so that might be a consideration if you have an older computer.
- Radar was more advanced in the U.S. fleet boats, and it was the primary method of acquiring targets. I like using the combination of radar and sonar when plotting an attack, especially when an "end around" is required to set up a convoy strike. If you prefer working mainly off the hydrophone, you may like SHIII better.
- The Pacific map is much more tactically interesting to me, with all those little islands and choke points for navigation lanes. The map is dynamic too, with shifting areas of control between the Japanese and the Allies as the war progresses and Japan is gradually pushed back to the home islands. The European campaign map is much more static by comparison, and I end up always going to the same areas to hunt convoys.
- SH4 has the occasional special mission in addition to tonnage goals, like dropping off insurgent supplies, or picking up downed air crew, or photographing harbors. The RSRD mod makes this even better.
About the only thing I don't like in SH4 is the long transit times to base, even with time compression, due to the size of the theater.