There were some updates for about a year. If the version you played had 4 optional bosses, most of the stuff after that was just bugfixes.
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Size: 900x700 | Tagged: safe, artist:rydelfox, bangles (g1), blossom, blue belle, butterscotch (g1), chief, cotton candy (g1), crumpet, firefly, fizzy, fluttershy, galaxy (g1), gusty, heart throb, majesty, masquerade (g1), medley, minty (g1), moondancer (g1), morning glory, north star (g1), powder, snuzzle, sparkler (g1), spike (g1), star swirl the bearded, steamer (g1), sunbeam, sunshimmer, surprise, wind whistler, g1, g4, female, filly fantasy vi, pixel art, sprite
Size: 900x700 | Tagged: safe, artist:rydelfox, bangles (g1), blossom, blue belle, butterscotch (g1), chief, cotton candy (g1), crumpet, firefly, fizzy, fluttershy, galaxy (g1), gusty, heart throb, majesty, masquerade (g1), medley, minty (g1), moondancer (g1), morning glory, north star (g1), powder, snuzzle, sparkler (g1), spike (g1), star swirl the bearded, steamer (g1), sunbeam, sunshimmer, surprise, wind whistler, g1, g4, female, filly fantasy vi, pixel art, sprite
Some details on certain ponies:  
Majesty was chosen for Phantom because she has magic horseshoes that can make her invisible  
Gusty was chosen for Kirin due to matching its color palette  
Starswirl and Powder had specific limitations on their pose, since they had to match up with the existing attack animations  
It can’t be seen here, but Firefly is animated in-game  
The 6 ponies for Legacy were the first 6 MLP toys released  
Most characters are trying, as best as pony anatomy allows, to match the pose of the original esper.
Size: 248x170 | Tagged: safe, artist:rydelfox, crossover, filly fantasy vi, pixel art, simple background, sprite, white background
Size: 248x170 | Tagged: safe, artist:rydelfox, crossover, filly fantasy vi, pixel art, simple background, sprite, white background
@Red-Supernova  
Not a coincidence - EarthBound is one of my favorite SNES games, and I made the MLP hack for it (EquestriaBound)