Personally, I found PoE2's system the absolute best I've ever played for a cRPG (better than BG, DOS, PoE1, and even Pathfinder). It feels just right and smooth.
The problems, IMO were:
1) PoE1 didn't have such a great system when it was released and it took several years of patching to get to a good place. People might have feared the same would happen from PoE2 [I really didn't like PoE1 the first few times I played, but after patching was done, I managed to finish it) and probably didn't know about PoE2 superior system.
2) The Pirate setting is not something I particularly associate with fantasy nor I like that much. I skipped all of Piranha's Bytes [the makers of Gothic] "pirate themed" games for that reason. It's not because it's "too modern" (I loved Arcanum).
3) The Naval management system was very simplistic.
4) I would have preferred moving around with Teleports, flying (Wings/Transformation spells, Flying spells, magical mounts). Comparing that to a "mundane ship" you can see how unappealing it really is.
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