1 Poor graphics
Final fantasy VI has very poor graphics compared to Final Fantasy VII and later versions of the game. The game was very appealing at its time because people at that time never saw better graphics.
2 Too many characters
The fact that the game has too many characters prevents people from connecting deeply to the important characters in the game.
3 Easy and not challenging
The battle system and the battles in FFVI are considered relatively easy. Many people have found it not challenging enough.
4 Kefka can't be taken seriously
Some fans have expressed their dis-contempt with Kefka, the main villain, as they couldn't take him seriously. According to their opinion, Sephiroth was seriously dangerous.
5 Nothing special about the game
The game had nice music and relatively interesting story, but apart from that, there was nothing very special about the game that could make it stand out.
6 It was good at its time
One of the factors that made the game successful is that it was released at a time where it could have easily been considered the best. This is the same thing that happened with Chrono Trigger. (See Why many people like Final Fantasy 9?)
7 Nostalgia led to excessive praise
Some people still idolize the game because of nostalgia. In such a case, the game reminds those people of the good old times.
8 Music is not good enough
The music of FFVI is good, but according to many fans, it's nothing compared to the music of FFVII.
9 No real direction
For a big part of the game, the characters move around with no real direction. The direction develops later in the game. (See Why Some people didn’t like Final Fantasy XV?)