The gamę is choppy because it's poorly coded, the flash cart has nothing to do with this. Using a more recent emuNAND might help due to performance improvements in the OS, that's your best bet.
I see... it's just strange that nobody in the internet has raised the problem, i read various forum and noone that has blamed the framerate, and its VERY noticeable in 2D :/The gamę is choppy because it's poorly coded, the flash cart has nothing to do with this. Using a more recent emuNAND might help due to performance improvements in the OS, that's your best bet.
Ok, i have updated the emuNAND at 7.2 and... yes, the framerate il better, there is less stuttering, in some areas you can clearly see the differences like the Death Mountain, in this case the framerate is perfect in 2D mode.You should absolutely use emuNAND for best compatibility, be sure to follow instructions carefully so that you don't update the real NAND by accident. Filters are usually disabled in 3D mode because soft edges interfere with the parallax effect, enabling them would spoil the depth effect. The only things that might be affected by a slow SD card are streamed content and loading/saving times.
Okay so I did a test, especially in the area you mentioned in Kakariko (including that house). For this test, I did immediate 2D and 3D comparisons, in the middle of the day (as opposed to evening, night, etc), and kept brightness on full with power-save mode off, in case that makes a difference. I also tested as both a kid and adult.
And I don't know... I'm not the most frame-sensitive person in the world, but I really don't notice any performance difference between 2D and 3D. The frame rate looked identical between the two, as far as my naked eye can tell.
Anyway, I hope this helps you in some way.