This one is a much more significant overhaul than the IV DS remake, and for the most part does a really good job of modernizing the 8-bit game, which had become incredibly dated. I like the characters they created for the main cast (who were basically 4 nameless/faceless protagonists in the original) and that they got rid of the annoying job point system from FF3, where it cost a grindable resource just to change jobs. It's a really solid game, overall. But it's also just faithful enough to the original to carry some of its baggage, and in the transition to being a FF7-style 3D game they messed up the pacing.
Basically, the random encounter rate is too high, and each battle takes too long to transition into and out of.
Think about what happens when you go into a random encounter in a 2D Final Fantasy game. There's a quick animation, then your characters and the enemy are on the screen, and immediately the command dialog pops up. You hold down the A button and your dudes do a tiny sword swipe animation, and then the enemies die, some boxes pop up telling you you got XP and gil and an item, but because you're holding the A button they're instantly dismissed and you only see them for like a frame. The whole thing can take like 10 seconds if you're in a low level area and one-shotting everything.
Now think about what happens in Final Fantasy VII. There's a flash, a transition, and then a slow, unskippable camera pan over the battle field before the camera assumes its fixed position. You hold A, mostly the same thing with the attack animations happens, but because it's 3D and your character has to move up to the enemy to hit them, the animations are all longer. Only a few frames longer, but these frames add up. Now you win the fight, and there's an unskippable "victory" animation showing your party, and there's a fade out, and a fade in to a "rewards" screen. It tallies up your rewards, and then fades back out. For the exact same low level fight you did in the 8-bit version, you've now spent over 30 seconds.
It doesn't sound like much on its own, but over the course of the entire game, and with the encounter rate as high as it is (it often feels like you're into a fight every 3 or 4 steps), this really starts to wear on you. Especially near the end when you're starting to fight much more difficult enemies that you can't just auto-battle through.
If not for that big flaw, I think this could potentially have been much higher on the list.