SH3 with GWX and Commander gives a lot more graphic feel for the harbors and such, and a lot more options for crew names, ship names and all the things that make for better immersion.
SH4 with Ops Monsun gives a better looking crew and more of them, along with better looking everything else, longitute and latitude on the maps as well as more detailed grid locations, more realistic crew management (they actually change watch all by themselves), as well as more stability and much faster loading times.
Both have their advantages, and both have their problems. For that reason I switch back and forth on a fairly regular basis.
Oops, waffling again.