The couple things I've noticed straight off the bat are:
1. The number of enemy shipping you come across is higher in SH3(GWX). Although, coming upon task forces/battleships/major historical battles is higher in SH4(TMO with RSRD). In general you'll have more random shipping to sink in GWX, but more military ships to sink in RSRD.
2. The graphics are obviously better in SH4, and I can't run SH3 in my native resolution of 1366x768, so it appears odd. The sea bed and the sea in general just seems more alive in SH4.
3. The fact that most Pacific subs start out with air radar, makes enemy air less annoying.
4. The User Interface(or HUD) is a lot easier to use in SH4. Basically some actions that require you to click two to three different things in SH3 have their own button in SH4.
5. The fact that the game has "watches" in SH4, makes crew management a lot easier than having to drag crew back and forth.
6. U-boats seem to dive faster than Fleet boats, although I'm unsure if the U-boats in UBM dive as fast as they do in SH3
7. SH3Commander is definitely a plus for SH3. You definitely feel more attached to your crew in SH3.
8. The RSRD campaign is very well done, a lot better than SH3 campaign.
9. In terms of sound, they both seem about the same. Although SH4 can realistically simulate how long it takes for sounds to reach you(unsure if SH3 can do this)
10. Time compression goes a lot higher and works a lot better in SH4, and it's easier to Refit and refuel.
11. A problem I had with SH4(RFB 2.0) that I've never had with SH3(GWX) is that I saved in the middle of a patrol while going ahead standard. Upon loading the SH4 save at a later point, my sub took damage without any explainable reason(There was nothing around me, and I was away from any land masses.)
As I've yet to sink a ship in SH4(TMO) I can't compare the combat. Although I'm unsure if Auto TDC works in TMO. (I can't do Manual in any game yet). My first patrol with TMO and RSRD ended up with me coming upon a Large minelayer escorted by two destroyers. I found the minelayer with my attack periscope and locked on(atleast I think I locked on) and fired all 4 torpedos before diving and changing course. All 4 torpedoes missed. Although this might have to do with my distance being so great, and other operator errors than the auto TDC not working. Going to set up a training mission later to test combat.
Overall SH4 is definitely a major improvement over SH3(unlike SH5 over any prior version
). Although in terms of immersion and feeling like you're part of your crew, I'd have to say SH3 is better.