First of all I know the fact that they are basically the same except the 3D functionality & form factor, but here's this article:
Zelda series producer Eiji Aonuma has said that the development team at Nintendo EAD Group No. 3 only found out about the existence of the Nintendo 2DS after starting work on The Legend of Zelda: A Link Between Worlds--which makes heavy use of the 3DS' 3D feature.
Speaking via an interpreter in an interview with GameSpot, Aonuma said that the team subsequently made some changes to ensure that the game was completely playable in 2D. "It's not that you can't play it with 2D, it's just that it becomes clearer when you have the 3D effect on. We found out about the 2DS during development, not before, and we also made changes so that we were sure that you could still play and solve the puzzles only with 2D. It's definitely still playable in 2D!"
blablabla 3D is great blablabla
From the bold part, the presence of the 2DS makes Zelda developers think twice before implement a game element that utilizes the 3D effect (like puzzles) so that 2DS owners can enjoy the same experience. As much as I think the 3D effect is a useless gimmick, there's nothing wrong with devs trying to be creative and take advantage of the feature (it might work idk). However, now that the 2DS is here, it probably won't happen.
On the contrary, supposedly a 3rd party developer utilizes the 3D effect and somewhat forget the existence of the 2DS, this might mess up the 2DS version since it will be much harder (or impossible) to solve the puzzle without 3D functionality; thus not as enjoyable as the 3DS version.
I think one solution to this is to strictly develop 2D gameplay elements for both the 3DS and 2DS and only leave the 3D as a visual option, it might prevent creativity/innovation this way however.
What do you think?