Have you uhh....
tried playing SNES games on an old 3DS?
I'm sure somebody in the homebrew circles is working on it, but honestly its kinda shoddy right now with the injects i've been using.
Most run fine (Chrono Trigger, FF6, MMX1) but there's a few with... issues (DKC, which I honestly only have a inject of to hold a space for the legit article).
Honestly the old 3DS just doesn't have enough juice. Remember how it had to do Smash Bros or MonHun4. I imagine something like that could be used for SNES but with how much of sticklers Nintendo are for accuracy I wouldn't put it past them that they can't get it working right.
If they couldn't get the Ambassador GBA games running the way they wanted I can understand why they held out for the SNES games. I understand it sucks but I understand why Nintendo did what they did for quality sake, hell even Mario RPG on standard emulators on computers has problems such as audio desyncing in certain places, so can you blame them for wanting to make sure evrything works?
I mean I doubt Pixel Perfect mode was the only reason, and to be honest not the reason I would go for for explaining why they could only make it work for New 3Ds, but there's much more technical lingo that they just don't want to explain due to how complicated it is, even though Pixel Perfect Mode makes less sense to explain tech limitations, it's just the reason they chose to explain, and not a very good one either.
Like I said I get why people are upset, I certainly do not blame them for being upset, and Nintendo definitely did not handle it very well with citing Pixel Perfect Mode as the sole reason they couldn't develope it for standard 3DSes. Not to mention the fact that you can't get a discount if you already have the games on Wii U because that is honestly a poor decision on their part that I agree with all too well. However people also need to understand that Nintendo just wants to make sure the games work right, lack of discounts and cross platform purchases aside because they really need to get with the times in terms of online services, but they know their own hardware better than we do and we have to understand that.