I did enjoy the GBA version, but there are legit reasons people dislike it. Namely-
1- the graphics received the traditional GBA brightening
2- actual graphics are a strange mix of the SNES and PS1 game. Sprites are from PS1, as are battle scenes, but environments are from the SNES game
3- many of the awesome little environmental touches such as water/mirror reflections are gone (several times, reflections are used for story reasons, so it looks lazy), there are a lot of missing graphical effects. No shadows and removed lighting effects. Golden Sun did better...
4- butchered sound (and there have been amazing GBA soundtracks, so it's not a good excuse that it's on gba and sounds like this)
5- slow clunky battle physics
6- bad translation, with horrid mistranslations (how did they turn Ragnarok into kangaroo???)
7- some of the worst voice acting ever
Even after all this, i still like the gba version. Dunno why...