In the original release for The Legend of Zelda: Oracle of Ages and The Legend of Zelda: Oracle of Seasons the games supported some extra content when played on a Game Boy Advance. Is that the case with the downloadable versions for the 3DS as well?
The 3DS version is the original GameBoy Color version (so it's missing the Advanced Shop, but you can edit your saves to add in the exclusive rings).
All of the colouring tweaks found in the Advance version are also missing.
GBA with the Advance shop open on the left. 3DS Virtual Console version on the right.
I did not find any official source yet, but there is a sufficient amount of people on the internet complaining about it to be sure that they are missing.