GBA version has 2 major flaws.
1. The music downgrade is way too noticeable. And we all know that is specially bad in a series renowned by its music.
SNES/PS:
GBA:
2. Even though they are 2D games, the FoV is smaller than their TV counterparts (SNES/PS versions).
(look at the 1:05 mark. It is pretty bad imo, it's all more crammed into the screen).
The battle screens also looks more packed in the GBA.
SNES/PS
GBA
Look at the space between names and ATB bars. Look at how much space above the tail the GBA one is missing.
Bonus: The colors can seem odd, specially if you played the other versions first. I prefer the darker palette (SNES, PS), specially in a game like FFVI.