1.) Having no option to skip the ridiculously long cutscenes in the older Zeldas. That annoyed me to death after I've already beaten the game and wanted to play it again. It takes FOREVER.
2.) Having a steamboat.
3.) Having a steam-train.
4.) FLOODING HYRULE. Hyrule is just so... so beautiful and magical and everything... And then the Hero didn't come one day and the Goddesses were forced to drown their creations. D: I can't stand trying to comprehend the fact that Hyrule Field, Hyrule Castle, and all of those other places are just GONE one day... I would play games like Ocarina of Time and look up at the sky... Thinking... One day... That is where people will live... And this is where fish will live. RARGH. >_<
5.) Having a limit on Rupees. (I agree with the people here!)
6.) Taking the Magic Meter out of the recent games. Seriously, what's up with that?! But in reality, though, it's not really the Meter I miss--it's the actual magic. The Meter limits your magic somewhat, but at least we had it. These days, with games like Twilight Princess, there's barely a hint of magic that Link can harness. D: I'd rather they bring back the full-power magic without the Magic Meter, since you always have to refill it somehow.
7.) Making bosses bigger but not badder. (TP, mostly. XD)
All I can think of for now. :3
(I don't really have a problem with the boat and the train--I just think that Zelda would be better off without them. It kind of ruins the Zelda-magic feel, in my opinion. :3)