Sorry for the late response, I just saw this project now! It's looking very neat!
In response to the person who said that bosses should be replaced, I would have to go against this. I love bosses in games, especially Zelda. Now, it would be nice to see some changes. I understand that you said you don't have the ability to modify bosses and make new ones, like URA is doing, but you should be able to mix it up a little. Add some traps into the room, put some normal enemies that spawn in during the fight as minions for the boss. Imagine if Twinrova could summon Torch Slugs and Freezards. I'm sure that you could design some things to make the bosses even more interesting. What if you added a bit of a puzzle element to the fight? Unsure how you would do this, though. Imagine if something like Barrinade had an ice barrier around it in its stationary form, that you had to use fire arrows or something similar to take off in order to hurt it? Little things like that, and spawning minions could make the bosses interesting.
Another thing you could maybe do with bosses is have the fights with them be elsewhere in the story? We've seen this with the Ganon in Lon Lon Ranch video. Maybe fighting some of them twice? Imagine if you fought Twinrova with a small modification in the Spirit Temple where you normally fought her, and then again toward the end of the game somewhere before Ganon with even harder modifications.