I play both regularly, and right now I'm only using u-boats in both. SH4 is better than SH3 in almost every way, but so far no one has made all the graphics goodies the the later game.
SH4 has several great mods for the Pacific side, and a fantastic campaign in RSRDC, plus one outstanding u-boat supermod, Operation Monsun. What SH4 doesn't have is a lot of the cools stuff to look at, and it doesn't have anything like SH3 Commander. That is all mod-work, and not intrinsic to the game, so the only thing wrong with SH4 is that modders keep ignoring it.
If it had those things I would shelve SH3 and never look back.
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