Ilia was fine, but I think what we needed here was a little more interaction with Link to make their relationship more believable. Perhaps she could have been captured during a later segment in the game.
For Tetra, I honestly would have left out the transformation entirely. Having her inexplicably turn into a princess and do a 180 in personality completely killed her.
Now to bring something new to the table, I would add something to the Lon Lon Ranch arc in OoT. It always seemed strange to me that when you beat Ingo, everything just suddenly goes back to normal: Talon is allowed to come back, Ingo is nice again, nobody asks any questions. There's definitely a piece missing here, like a final confrontation with Ingo where you free him from a corrupting influence or just beat him into submission.