I play both, so I hope I can give you a fair comparison.
The Good: Nicer graphics, automatic crew rotation, 'Battle Stations', which puts the entire crew on alert and the best men of each team into their assigned compartments, the much nicer 'M' key which brings the message to you rather than take you to a 'Radio Room' screen, and probably a few more that I'm forgetting.
The Bad: SH4 doesn't have a multi-time-zone clock like SH3 does. SH3 shows GMT but if you pass the cursor over the time it also gives you local time, which changes with each time zone. SH4 gives you the time at your home base, and nothing else. Others have reported differently, but it has been my experience that I always have the exact same start time for every patrol, and I think it was 1100 hours.
What's missing: Lurker has done a stellar job with Operation Monsun, and it is great fun to play. That said, there are a couple of things he never got to finish. All officers in OM seem to have the same rank. The type II has 44 men. The correct number should be 25 for the IIa and 28 for the IId. SH4 also never got the attention from the modders that SH3 received and still does. Most of this is fluff, but it's fluff I like. The Kiel Canal is a big empty river (at least there is a canal, which stock SH3 didn't have). No locks, no gates. Not a lot of traffic in the harbors. None of the fun little goodies that GWX, LSH3 and WAC give. I'm sure the AI is okay, but nothing like NYGM's. No SH4 Commander. SH4 is better than SH3, but it doesn't have the flair that all those mods bring, and it seemingly never will. If those aren't things that matter to you, you'll probably love SH4 with OM.
If SH4 had all the mods benefits that SH3 does, I'd put the older game on the shelf and never look back. But it doesn't, so I still play both. I like SH4, but for the reasons stated I don't love it. On the other hand I still sometimes play Aces Of The Deep and Silent Hunter 1.
