No they're all emulated besides GBA games on the 3DS. That's why you can extract roms for them. Especially with Gameboy Games. They use to have an exploit that let you swap the rom used using the web browser.
There's nothing for them to fix. The way GBA games work is the same as how DS games work on the 3DS. From what I know about it you can't access the home menu while playing GBA games on the 3DS just like when playing DS games. I suggest actually researching this stuff before making claims.
I specifically meant Wii Virtual console, but whatever... anyways, it runs almost the same as a GBA game on the DS system, they have reasons for this, part of it has to do with the fact that most of the GBA games that were released on the 3DS VC were originally meant to be run on 3D, and do run in 3D if you had the Nintendo Ambassador's program, still, yet another reason is to prevent the game from saving improperly, as with the N64 VC on the Wii, (which, some games still glich improperly when you press home while saving) anyways, I should do more research, but there's still games like Four Swords that use wireless and are Gameboy Advanced games, and they technically aren't emulated either. Nintendo can change the rules for their Virtual console at any time they decide they have the resources to do so.
They technically changed the rules for Pokemon Yellow, Red, and Blue, and I'm sure they won't be including restore points for these games.
Edited by NarnianKnight, 19 November 2015 - 10:15 PM.