That's the issue with Nintendo games in general, they'll alter things slightly to give a fresh take and fans gobble it up. I actually heard "I thought it was clever how they got Zelda this time, it surprised me!"
How about the princess isn't a bloody issue? Or she is the bad guy, or she's helping you, or she's out doing the same thing you are from the other side of the world so you two can meet up, or you play as her!
Then again the fanbase is so against change I've seen threads outraged at the female Link concepts. I enjoyed Hyrule Warriors because Link was hardly the focus. Playing as any of the characters you felt far more strong than Link and like you were able to do more. (Though hardly true since his spin attack is so stupidly over powered)
This kinda is the feeling I've gotten with Twilight Princess as well, Link isn't this mighty hero who has to do all of this alone, Midna is essential to him getting things done. She's also a character that actually has some kind of arc and grows vs the other games. (I haven't finished this game so do not spoil this please.)
Every fan likes to bark at me how great Ocarina of Time is vs any game including other Zelda games. I say bark because they usually freak when I say I don't agree that it's "the best game of all time" so instant fanrage. I think it's fairly subpar in ways, the story is incredibly non-existant, there's not a character in the world to care about except Zelda and maybe the green haired girl. Like you said OP, Zelda was doing some work behind the scenes and was getting things done, then PLOT HAPPENS, come with me. Oh Link just ISN'T worth my time capturing, what could he do ...besides stick a sword that's murdered my face a bunch of times in my face. Yes, the gameplay was fine but weak plot and story means it's not the perfect game, it's just something reviewers are scared to make a note against because they know fan outrage will be high.
Either way, it's a fun series that just could do with some change ...like you said, Zelda not being abducted.