Okay, here we go:
Virtual Console is emulation. IE, there is a software interpreter that does the running of the games. This is incredibly taxing on the hardware and resources. I think estimates that I've heard once, was that to get anywhere near "good" emulation, it's about 5x the resources.
The GBA isn't being emulated. The 3DS hardware natively is able to execute and run GBA binaries. There is no emulation. It takes advantage of the second processor in the system to be able to provide you with return to home menu functionality. In fact, if it WEREN'T for taht second processor, you'd have to shut the system totally down just to get back to Home.
The 3DS (dunno about New 3DS, but that's another story) cannot emulate the GBA quickly or accurately. Could it run a game? Sure. Would it be glitchy and run at less than fullspeed without a fuckton of hacks that ruin features in a lot of games? Definitely. I'm sure you can see how this is far from ideal.
The SNES is even more powerful than the GBA. Better sound chip, better GFX chip, better CPU, everything is basically just straight up better, particularly when it comes down to raw specs. Now, the GBA's CPU might be more modern, allowing it to do more things with a single clock etc, but that's doesn't mean jack shit when you're trying to emulate, since you pretty much have to emulate what the other machine did, ie, what it did in 3 clocks, you have to emulate those 3 clocks. So if the 3DS can't EMULATE the GBA, what makes you think it can emulate a beefier system?