Besides having better graphics, SH4 also has automatic crew management. It also runs better. I can't run SH3 above 1024 TC without having major problems. I can run SH4 up to 4096 TC with no problem at all. SH4 also only loads a 6-month period surrounding the start date, rather than loading the whole war, so it loads faster and runs smoother. I've been playing Operation Monsun for awhile, and it's a very nice campaign, but none of the cool SH3 stuff is there. The harbors are pretty naked, and none of the cool things like Privateer's blimps have been ported into SH4.
I have felt for a long time that it is by far the better platform for all these mods.
But of course that's just my opinion.