They changed some bosses up, most notably Twinmold, and I also remember the bank in Clock Town being located in a different (and much easier to find) place. The boss changes were weird, though - they mostly just received huge eyeballs that pop out when they enter the "hit me" phase, which was really pointless, and then Twinmold, well, they changed the whole battle by making you get the giant mask only halfway through it.
They redid the boss battles and there were other changes like the Bomber's Notebook (Which is overall good in the remake, but the constant notifications quickly started to annoy me). If you have the time, this video explains perfectly all the changes (And funnily enough, it's by the same guy who's making the HD textures):
I guess I just remember the good changes being so much more beneficial that any negative changes were moot.
Like the bomber notebook being a huge plus. Before it, felt like you needed to bring out a guide online to accomplish everything. The new game, its like an big rpg, you talk to someone your journal gets updated (or in this case bombers notebook)
The bank being easier to find. The song letting you skip to exactly a time versus was it just half day increments before? Ect.
An eyeball on bosses or not being able to spam swimming or a couple others is a small insignificant price, imo, to vast life improvement changes.
My biggest hate with MM or Ocarina remakes are always just the ocarina. I still have to this day the songs memorized on the little c-buttons on the 64 controller. I hate pushing like LR and shit to play a song. Before it was so easy. Just yellow up, left, right, donw, or green and red button. Now its LR, LB, x, y, a, b. Add onto the other system controllers wher eI get x and y buttons consumed a lot and it just annoys me.