Okay, thanks for the reply, good info! That's what I figured about GBA games. Seems for now my best options are to play on my DSi XL and my actual GBA if I want the clearest picture.For GBA, those are the only two options. Small letterboxed or fullscreen blurry, it's just not physically possible since the 3DS is 1.5x the resolution of the GBA so better scaling isn't possible.
For SNES it should be more or less pixel perfect I think, the SNES outputs at 240p and that's what the 3DS is too. If there's any scaling it's probably just horizontally scaling to the proper aspect ratio of 4:3 since due to the way CRT TVs work the SNES outputs an image that is 8:7 using square pixels, however CRTs don't display pixels like a digital display so that 8:7 image is actually drawn with non-square 'pixels' at 4:3 aspect ratio. There might be some option somewhere to choose between square pixels and scaling 4:3, but I'm afraid I'm not sure exactly.
Regarding the SNES, I will definitely have to look into whether there is a square picture/4:3 scaling option in NSUI. I did a recent full playthrough of my 3ds-injected Earthbound (with the MaternalBound vanilla+ rom hack- highly recommended btw), and at the time it looked really clear and crisp but I booted it up again today and the text did look a little fuzzy. Could totally be just my mind playing tricks on me or perhaps the original game looked that way? I attached a couple of screenshots. The last one is a screenshot (with the Teddy Bear on the left) I grabbed from Google for comparison.
Am I just nitpicking too much? Probably