The Forest Temple gave me no end of grief! It was harder than the Water Temple for me in some ways, but not as much of a headache. I'd love to see an improved Water Temple, new minigames too.
Back when the DS originally came out I had a dream of seeing it ported over like Mario 64, I had even worked out design ideas for how buttons could work and such. One of my ideas also involved a separate minigame menu where after you played that minigame in the main game it would be unlocked there, and with multiplayer. IE: best times for like the Chicken catching game or the horseback target shooting, and maybe a multiplayer fight system where you could use semi-custom characters. Something like you could chose from different hats, faces, cloths, colors for cloths, weapons, etc, all for simply looks and individuality. Maybe that latter idea was a longshot, but I could see some kind of extra minigames added, and some competitiveness would be welcome.
I'm the kind of guy too (to go back to extra gameplay) who likes to see additional content added to a remake. I think the main story is too important to really mess with anything in there other than dungeon retooling, but maybe something like an extra post game mini-story could tie in well. Maybe add in an extra dungeon and do something to bridge the story between OoT and MM and leave it hanging right where MM picks up. That would work out perfectly too if they decided to remake MM too. Build up some extra hype for that.
And lets think a little bit farther too. Remember when we were given the gift of A Link to the Past on the GBA? We were also given the first iteration of the Four Swords with it. And upon completion of Four Swords we got an extra ability in Link to the Past. Maybe they could work in something similar. Have a Wi-Fi co-op enabled Four Swords with an OoT bonus once you finish it. There is allot of potential for SOMETHING awesome to be worked in like these ideas. They have 2GB of game space to work with, and as amazing as it is I don't think just OoT would take up all that space. They don't HAVE to use all the available space, but I think a game like this deserves it.