For weaker devices like the 3DS, specialized applications are generally better, assuming the work is put into it. The problem is, that's a lot of work to get to that point. Especially considering whoever develops the homebrew software won't make money off of it. Maybe through donations and ads, but that's still not much, especially for the time and work.Basically why I prefer original apps like this one over Retro-Arch; at least this one was going somewhere.
Also, would it be worthwhile to reverse-engineer the coding for the Pokemon RBY VC link cable coding into this? I understand it's written specifically for the games in question, but having at least some insight into how we could get link cable features working for the 3DS is better than nothing.
As for the link cable, I really don't know. Reverse engineering isn't as simple as it sounds. I think online linking could be done, but I don't think anyone has figured the 3DS's local ad hoc yet. Though, if you're near a router, that wouldn't be a big deal. Though, the GBC's linking was really sensitive to latency. Online play might require some impressive trickery to get working. Either way, at this point, I'm starting to pull shit out my ass, so I should probably stop thinking about it.