It's been mentioned, but I allow myself to point it out again: Dangerous Waters.
I don't think the SH3 engine, nor any drastically updated engine, could possibly cope with the extreme amounts of data that is needed to make this realistic.
I would have loved a merged SH/DW, because in DW you need to invest quite a bit of time and work to obtain good results, and you can only travel so far. Also, there is a lack of shipping that makes it very annoying to read that the game possesses "270 different ships/vehicles", while most of these 270 are just the same ships belonging to different nations. Also, Sonalysts can only invest so much time in updating DW, since it's hardcore, and not necessarily very fun for the standard gamer, which in turn means it doesn't sell like hell.
It's quite annoying that they've put in the old Type 206 diesel-electric German, when the 209 and 212 are FAR better adversaries, and the 212 virtually invisible. There aren't too many bugs, though. Just limitations. ARRRRRRRRRRRRRRRGH!