With as awesome as this game is (This is my second fave Final Fantasy besides VII) I wonder, is there a chance that some other Square RPGs to be hacked. Like say, Secret of Mana, Chrono Trigger, or Final Fantasy IV?

A Chrono Trigger pony mod would be fantastic as that is another of my favorite games on the SNES that I played!

I can tell you now that a Chrono Trigger Mod would be a bitch to make. The sheer amount of spritework in that game is absurd, and the game isn't that friendly to customization: IIRC all the maps are single planes of a predrawn background. Not the Tiles that FFVI uses. and like FFVI its engine is pretty broken. both in combat and in overworld exploration. And all encounters are predetermined, meaning you'd have to map all those out too.

Secret Of Mana has similar issues as well, but is a bit more flexible since the engine is a bit more loose and a lot more of the assets can be reused. Plus Secret of Mana's art-style blends very well with the FiM artstyle, Monsters will barely have to be touched.

The ease or difficulty of modding graphics, sprites or other graphical related aspects of said games aside, another difficulty would be implementing a story based in the FIM universe that is believable. FFVI just so happened to fit in the context of FIM fairly easily so the story did not have to change much (though it should be noted that the original Pony Fantasy VI set the whole game in a separate universe where all characters did not know each other before hand so that is an option though a bit of a flimsy one story-wise).
As far as changing the story for say Secret of Mana for example, one might resort to using non-main (non-"mane") characters for the story to work in a believable context. Chrono Trigger... Oh boy. Where do you even begin with modding the story in that without using entirely original characters? Final Fantasy VI? Not as difficult perhaps. It could work in the context of Cecil being played by Thorax and his brother playing Kain for example or perhaps in the context of Tempest Shadow as Cecil and Storm King as Golbez or something while working in the Pony of Shadows as the final boss. I know someone wrote a fanfic crossover with the ponies as the main characters but I think it is essentially set as a separate universe like Pony Fantasy was. Heck, using the pillars in the context of one of these games could be an answer of sorts.

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If I ever pony hacked another game, it would be Secret of Evermore as a "Human in Anthro-Equestria" adventure. Make the three realms into one for each pony tribe, the Mane Six can be divided two each, Celestia as Ruffleburg with Luna as Carltron. It could work.

I know someone else is making Filly Fantasy IV, don't know his story concepts well though.

https://thepatrickinator.deviantart.com/

But since you got me thinking about it...

Cecil - Twilight (Twilicorn for Paladin)
Golbez/Theodore Harvey - King Sombra/Shining Armor
Kain - Sunset
Rydia - Starlight
Tellah - Zecora
Edward - Fluttershy
Rosa - Spike (be a fun flip on the "White Magician Girl" idea)
Yang - Applejack
Palom and Porom - Pinkie and Rarity
Edge - Rainbow
Cid - Spitfire
Fusoya - Star Swirl
Zemus/Zeromus - Stygian/Pony of Shadows
The Archfiends - The Nightmares
Scarmiglione - Midnight Sparkle
Cagnazzo/"King" - Chrysalis/Cadance
Barbariccia - Nightmare Moon
Rubicante - Daybreaker
Dr. Lugae - Kibitz
Dwarves - Changelings
King Giott and Luca - Thorax and Pharynx