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This one has the best combat (aerial combos are so good here!), best exploration (jump in 3D space, gather spirits to keep upgrading your islands, loot respawnable chests, etc), best GFX, best crafting/fishing mechanics making it more engaging and immersive (timed button presses whereas the rest of the series doesn't have that) and arguably the best music too.
The planting system, while interesting and fun on its own right, does not come even close to making up for the lack of actual farming. This is the 1st huge flaw in the game and the main reason a lot of people don't like it.
The 2nd big flaw is the way "world map" exploration works. Because you can only teleport to your Golem outside town, you're essentially stuck exploring 1 place for a while OR places close by and every time you want to explore far away islands it will take a long time to move the Golem there (not real time, but in-game time). In short, this teleport system is too intrusive and affects enjoyment negatively.
The 3rd big flaw is that the female protagonist can only be played after the story is over. Still, at least this game has a female playable character (and it's the only 3D RF to have that) PLUS there are cheat codes to play as her from the start.