This is more of a 2D vs 3D debate for me. If Nintendo kept making games for the 3DS that were like OoT3D (by this i mean a 3D Zelda game) then i'd have no problem playing a handheld Zelda as opposed to a home console Zelda. I still have my N64 and while I was worried that OoT3D would destroy the original magic, it really didn't, and so I know that the 3DS is capable of having many more 3D Zeldas on the 3DS. BUT to Nintendo the handheld market seems to be the home for 2D Zeldas, which is a shame because i feel the 2D Zeldas to be very restricting after so many.
It also seems as if Nintendo are adamant about keeping the WW style for the DS/handhelds too, (which worries me that we'll see an SS sequel or two or at least a fair few more games in the graphical style of such) as opposed to the OoT, TP style graphics. which again is a shame, Nintendo would sell a lot more Zelda copies and consoles if they were to make 3D Zelda games across the board. But we'll see many more 'toon' 2D Zelda games for a while yet, until one of Nintendo's handhelds become so powerful that they're mini ps3s, in which case there will be no need for 2D Zelda.