I didn't really grow up with the Zelda games but I have been playing them a lot lately in order (almost done with WW now, so just TP and SS to go; and maybe go back to TAoL but... meh), and I have noticed a few things that would make a new Zelda game a lot better in my eyes.
1) Less stressful mini-games. Mini-games should not take more than 20 attempts to beat, especially if they are based solely on luck or things that had nothing to do with playing the game (so I will give a pass to targetting mini-games) but mini-games like the letter-sorting mini game and the battleship mini-game (I forget what it was called) annoy me a lot because they are designed to take a lot of attemps and have very very little in common with the core game. My rule here is if it takes more than 10 minutes for the average person to complete, relax the restrictions a bit so it doesn't, even if it means not using a round number (OMG THE LETTER SORTING GAME WOULD HAVE BEEN A MILLION TIMES EASIER IF IT HAD EITHER BEEN 24 LETTERS OR 31 SECONDS).
2) Regular controls as an option if going back to the old scheme. I don't know if I am the only one, but I hate inverted controls and can never get used to up being down and down being up. I don't know if TP had this option, and it looks like the WW HD edition will have this option, but it is so neccessary I think, or at least pointless not to do, so I put it on here.
3) Fill up the sky/sea/whatever. Not a biggie, but if you are going that route, fill it up a bit more so you aren't traveling that long to get to your island.
4) Voice acting please. I am sure this will be a controversial one, but voice acting would be so much better. You can even keep Link mostly silent, but it would still be cool to hear those around him. Lots of classic series have done that, there is no reason Zelda couldn't (other than of course the fact that it has sucked when they have done it before).
I will try to think of some other things, but those seem like the biggest ones that they have struggled with in the past. Let me know what you think.