The main story of 6 is really good, and those are the parts people remember fondly. I think the main issue narratively is that they didn't do a good job setting up for the World of Ruin. The story is entirely front loaded and then you get to wander around the whole world (which still has a designated path you're really supposed to follow if you don't want to get wiped by random monsters), and Terra, the ostensible protagonist of the game, is for some reason just not important once you enter the World of Ruin? You probably will get her but you don't have to, and while she's a good unit nothing is narratively made of just leaving her to get ganked by Humbaba. And the bloated character list of FF6 is ridiculous. You have two blue mages, one that's actually useful (Strago) and one that's a huge pain in the ass to get going (Gau; seriously, look up how the Veldt actually works sometimes, trying to get even most of the enemy moves on Gau is a Herculean task), your designated swordsman character is worse at doing damage with physical attacks than your inventor, a super-powerful party member you can't control would be a neat idea, but Umaro isn't tougher than Mog and doesn't do more damage than Sabin. You could cut the FF6 roster down to like 8 characters and the game would be much tighter and more satisfying. In comparison, FF7 has one shitty character (Cait Sith) that isn't even mechanically useless and it's still a joke to this day.
All of this is to say, I think FF6 deserves more criticism for people being blinded by nostalgia than FF7.