Mostly agreed. The only gripes I have are that they nerfed the Deku Palace, where if you fall from one of the higher platforms while trying to infiltrate it the game voids you out and resets you to where you don't have to repeat everything; and they made Twinmold terrible. Apparently your mileage may vary on Twinmold but he's just not fun at all to me in the 3DS version.
As far as the Deku Palace, I was actually fine with that change. I don't fall down much these days, but young Anthus would have loved that. I also like how you can open up a shortcut to the bean seller. It's one of the QoL changes I was fine with. I do agree about Twinmold though, and even Ghoat to an extent. Really, the boss changes seemed really out of left field. Odollwa was okay, and I don't remember Gyorg fight.
I also never understood swapping out the graveyard bottle for the heart piece Madam Aroma gives you. It actually kind of confused me and my friend when we played since we both forgot.
EDIT: Oh! How could I forget? They totally nerfed, and ruined swimming with Zora Link in the 3DS version. Besides this stuff, I agree it is the definitive version, but if you liked it, I'd recommend the original too, if you have the patience for it.