I made a similar thread for the Wii U, but since the problem also exists in 3DS, and it looks different than the Wii U, I will have this thread too.
Basically, it goes like this:
PLEASE!! More people need to complain to Nintendo about this so they can fix it. I've already done it. We need quality in our Virtual Console.
And no, the game did NOT look that blurry in the original NES console.
We need an option to switch between stretch and normal pixels.
Thanks.