Nintendo basically has the opportunity to improve/modernize OOT with the 3DS port. Do you want them to? Do you want more content in an already enormous game? How would you go about it (besides the Iron Boots thing)?
I would update the movement speed and fluidity to Twilight Princess standard and make the enemies faster and craftier to match it. I would also just have more enemies. More enemies, better AI, some unpredictable behavior. Hyrule Field should eventually be crawling with danger. I would also make Hyrule Field something of a huge, seamless obstacle course for Epona (people love ridin' horses, right?), with Equestrian mini-games built around it. And I'd sprinkle more secrets and hidden coves and unmarked bombable walls and burnable bushes across the game world, maybe with new rewards for finding them. (Oni Link?)
Finally, (unlockable?) HARD MODE. And maybe even an ULTRA-HARD MODE. Something to make the people who think Zelda has gone soft cry. Increased danger, enemy substitutions, lethal bosses with new attacks... the whole enchilada. (Oni Link Mode?)
Plus, Master Quest should be thrown in.
Oh, and I'd like more mini-games, preferably leveraging touch control and the awesome power of 3D!! (Bozo Buckets?)
Oops, I forgot the most important part: FOUR SWORDS ONLINE (with a side of Phantom Hourglass online). Pleeeeease, Nintendo. To be honest, I'm not even sure I'll pick this port up, but Four Swords would seal the fuckin' deal.
Add in the ability to swing your sword while running (like in Twilight Princess). That aspect alone helped improve the flow of the game, at least IMO. And I like being able to switch your items using the touch-screen on the fly. Good on Nintendo for implementing that.
Other than that, I'm not expecting much. Maybe a new dungeon, which has been a staple for all Legend of Zelda remakes on Nintendo's portables. (not counting the NES GBA ports, which were.... well, ports, naturally)
I think the game is fine as it is - I don't feel much else needs (or should) be changed.
I used to really enjoy those 'blowing a ship across a river' mini-games in the early days of the DS. The timing-based ones with obstacles. Thought those were hella cool. I wonder if the 3DS' additional horsepower will allow for more real-time voice command.