Major Endgame Spoilers Below
Going to list the flaws of FFVII according to my experience of the game
-Story is not entirely explained / not a cohesive story brought full circle at the end. Had no idea it would be an abrupt ending and based on the incredible story given all throughout the game, I found the lack of story at the very end to be pure laziness. Why would you put all that effort into an otherwise godly game and neglect the ending? It would have been a tall order to fill for sure but they didn't even try imo
-Holy could have been explained better
-Marlene, a major reason for Barret's involvement in the story, is never shown again after the beginning of the game
-Aeris's foster mother also the foster mother of Marlene (essentially) as well, are never seen again after the beginning of the game
-Ending of game didn't explain much at all, it was just a cutscene
-Cloud goes from hardcore leader to a complete pussy for a decent stretch of the game. This could have been avoided or at least salvaged to some degree. Cloud had some really uncharacteristic dialogue at times
-Chocobo Sage is a fucking useless moron who can't remember a thing and wastes your time
-Chocobo sidequest in general is a waste of time and is over-complicated, takes too long to even get an inkling of an idea of what to do and how best to start this sidequest
-Yuffie's entire arc is just that she's a dumb (yet tough) teen who likes Materia enough to rob people blind, even her comrades who are clearly trying to save the planet. Her love for Materia and stealing it is more important than a task at hand that involves securing the safety of the planet. She crosses a band of heroes in a disgustingly irredeemable way. The player is forced to chalk it up to, "she's just a teen a stupid kid we must forgiver her" and the story moves on without anything else. Character development is an oxymoron for Yuffie. Her character was slashed and her image never recovered in the slightest tbh. She never did anything substantial enough to cancel out her treacherous stint as a Materia thief
-Cait Sith was even worse than Yuffie. Double crosser, liar, and what he did was give an item we could not get back so easily. Materia we can gain back, but what he stole from us put fate into the hands of the enemy entirely. Also, he essentially lead Barret away from Tifa and nearly had her killed. He didn't really help at all in that situation; Tifa helped herself out of the deadly gas chamber. All Cait Sith did was lead Barret away from Tifa
-The entire Turks and their pride thing was really dumb and went nowhere. Besides Rude being a badass at times, what were the Turks even good for?