I really like the game (the dungeons and art style are what sells it for me) but it certainly isn't flawless.
I completely agree on Fi. The techno-bable does not fit in at all well with the Zelda universe (she sounds like fucking GLaDOS) and she's nags way too much. Navi was also a pain but out of nostalgia somehow her nagging has become delightfully annoying.
The overworld is one of the worst Zelda has ever seen, not open enough. It doesn't feel organic. The hub with places off of it isn't a terrible idea and can work wonderfully (well it has once, in SM64) but they didn't pull it off.











