Your thoughts on the game sound very similar to mine. I'd be interested to know what obvious flaws and annoying decisions you're referring to. Some I can think of:
- Parts of the game that seem redundant, e.g. that annoying mission where you have to guard Scrapper just because he messed up.
- The usual problem of Zelda bosses being too easy even on the harder mode.
- Although it was nice to have much more interesting overworld sections, this made the dungeons feel unusually simple compared to the rest of the series.
- The usual issue of villain stupidity, e.g. they always create bosses to 'test' you at first, rather than fighting you while you're weak at the start of the game. The way Scaldera appeared before entering the boss room was cool, though.
- Fi's boring 'personality' compared to characters like Midna. I conjecture that 80% of gamers would find her boring/annoying.
- Many more...
It's also not my favourite in the series, but I'm not sure why. Possibly because I've played most of the series and the formula is now very familiar. For some reason Twilight Princess is still my favourite - perhaps due to the complex, diverse dungeons, the dark atmosphere, and more memorable cutscenes than in any other title I've played. Somehow TP felt like a bigger game to me, even though my recent play-throughs have been 18 hours at most, compared to Skyward Sword taking well over 30 even without sidequests. My second favourite is Majora's Mask, so it seems I have a preference for the darker storylines.
Also, I wouldn't call TP's graphics 'super-realistic' - more like 'a somewhat realistic style, limited by the hardware'. When we finally see a HD Zelda game, hopefully it will be deserving of that description.
the dungeons did feel much easier compared to the rest of the series. None of them came even close to how horrendously difficult Stone Tower Temple from Majora's Mask was for me.
I really enjoyed the sidequests in the game though. They were enjoyable, and I feel that people who rushed through the game without even doing them literally missed like half the game (it took me 71 hours to beat the game) that gave the game some more depth, if that makes sense.
also, being able to upgrade almost all your weapons/items is such a wonderful addition to the series. I also loved how the game actually had some hilarious moments (Groose, anyone?). Speaking of Groose, the game really had some memorable characters that played a major role in the story who were not named Link or Zelda.
but yeah, I found the guarding Scrapper mission incredibly annoying. and fighting (I won't say which boss) the same boss three times was annoying too.
I thought part of what made this game my favorite Zelda game was that because of the new controls, the enemies were harder to kill than in previous games, including the regular enemies.
Fi took some getting used to after Midna but she grew on me as time went on. It's pretty interesting to see her comments on anything you Z-target. Fun fact: she talks a lot like one of my friends. Maybe that's why I liked her lol.
One thing though: the overworld is much richer than in previous games. Also, this goes back to the sidequests thing but people really need to slow down and take a look around, do sidequests and stop and think of what you're doing, and even if what you're doing is somewhat simple, it's really freaking cool. Gah, I wish I could give examples but that would involve spoilers. Bottom line, if you want to enjoy the game, don't rush!