The graphics and effects in SH4 sealed the deal for me. I couldn't dream of playing without transparent water now.
Eye candy aside, I felt more drawn into SH3 than SH4. Can't put my finger on it but SH3 just "felt" more "real". Whereas in SH4, all the elements are there, but it just feels a little administrative. An example, in SH3 you manage the crew by dragging a little man shaped icon (it's actually a man

) into the compartment you wanted him in. In SH4, not only do you not need to manage your crew if don't want to, the icons are simply squares with little generic mugshots in them. Also, clicking on your 3D crew members brought up their functions. I think the SH3 system appealed to the GI Joe kid in me, moving your toy soldiers around, stuff like that.
I play Operation Monsun and enjoy the Atlantic campaigns. Hopefully the GWX team will work some magic and bring back the "feel" i miss so much.