Made an account because I need to thank you for writing this. Saw FF6 in Steam, and was devastated when I saw that it was a bad mobile port, but continually found I didn't have the right words to convey -why- it rubbed me the wrong way. Except the portraits. That one was easy to tell since they're static and draw attention away from the character sprites.
But here you broke everything down, showed the evidence, and explained it so perfectly. I lovelovelove the idea of being able to pick which way the game filters. I generally tweak filters when emulating anyways. I realize I prefer the blocky rendering much more than the smoothed out look (and good grief, yes, either are better than Squeenix's terribad middle ground).
I remember when I picked up the iOS version for sake of wanting to actually own one of my childhood darlings, I hated the sprites on first sight. A day later I stepped back and realized that they really weren't bad sprites. Could've been better, for sure, but they weren't bad. And now I can say I know why they rubbed me the wrong way at the beginning - preference for an unfiltered look, and the matter of 3 competing art styles. By itself, that sprite sheet of Terra's is downright adorable.
Speaking of sprites, (if you care about my opinion of someone who has no idea what game your personal remake project is, that is) I found the original, savage, toothy grin of that berserker character to be rather charming. I think some of it got lost in the redrawing, though... Referring to this picture: http://www.fortressofdoors.com/content/images/2015/09/xbr_pipeline.png
Maybe that's just me, but there's my two cents
Thanks again, and good luck with your project!