Something like Majora's Mask in terms of atmosphere (impending doomz) but I want more dongeons! I can't get enough of them... I mean take example of ALttP. There was so many of them (12, if I recall correctly, 4 in light world and 8 in dark world).
Oh and speaking of ALttP, I want bosses to be kind of like in that game. They could seriously kick your butt, you lose quite a few hearts when hit and they take more than just 3 hits to die! I want to really think of the best way to defeat them, along with using the dongeon weapon. The weapon found should be used not only creatively in the dongeon but also outside of it. Give them more purpose than just in one area.
I think Twilight Princess had some of the best characters and story (sorry people but I love those two elements) and although my favourite Ganondorf was WW, I found OoT's Ganon more imposing and threatening. It was huge and hitting so hard destroying everything in its path, you could only see glimpes of it when the lightening was hitting and it had red glowy eyes... I remember being so nervous fighting it. I just wish it was somewhat harder to beat. WW pupets (wtf) don't do it for me, nor does the warping boar of TP.
I'd love to see magic items come back. ALttP had so many of them, even though you didn't need them all, they were fun to discover and mostly, to use.
And finally not so importantly, the character design should be like TP but with a different art style. I like realistic graphics but something that stands out is more likely to look nice for a long time. As long as the characters don't go WW pumpkin heads (creepy) I don't have a problem with it.