The GBA version is a really crappy port. There's a lot of slowdown and a bad framerate during battle and the music sounds really, really awful (The GBC spinoff recycles like 90% of the soundtrack and manages to sound far better. Sad).
Many complain about the oversaturated colors but the game wasn't intended to be played in emulators and was made long before bright backlit GBAs came out. The "problem" isn't very apparent on the less vibrant frontlit GBA and DS screens.
The gameplay of the GBA version though is largely based on the PSX version, but the sloppiness of the port doesn't make it much fun. The lack of buttons compared to the PSX controller make for wacky button combos to be able to do important things like defend and skill shortcuts when needed. Although it has a few exclusives, it's missing most if not all of the new sidequests, dungeons, and optional battles from the PSX version.
Anyway, it's hard for me to pick between the SNES and GBA versions. I don't really like either of them that much. The gameplay is better and more refined in the GBA version but the slowdown hurts it pretty bad. The SNES version feels way too obsolete compared to the PSX version and later installments in the series to be any fun.
In relative terms of port quality (of ToP PSX to GBA), it makes FF4 GBA look like god.