Nintendo is currently working on getting more Game Boy Advance games on the 3DS eShop, according to Natsume.
Natsume Inc Community Manager, CeeCee, revealed this bit of information in a recent Q&A, saying:
No, Nintendo does not put recent console games on the 3DS eShop, and sadly that means we cannot either. The same goes with GBA (outside of the ambassador games) — though they’re working on this and we look forward to the day it’s possible. But until that day comes, we aren’t actively working on porting any specific GBA or GameCube games. We’re aware today that Nintendo has announced plans to launch DS games for the WiiU – it’s an exciting time, and we’ll be reviewing our DS catalogue for potential titles.
Nintendo is sitting on a gold mine of incredible games from generations past, and it's really a shame they haven't been added to the company's digital store. Here's to hoping we'll be playing games like Golden Sun and Advance Wars on our 3DSs sooner rather than later.