Okay maybe I was a bit abrupt. And since I originally quoted you and you want me to explain more, I will.
The variety- there's nothing like it. The game throws constant surprises at you. This is long before the term 'minigame' became a dirty word, and genre variety was not only accepted but welcome. The game is asking you to do weird, fun stuff completely unrelated to the core battle system frequently, far more than any other game in the series, or any RPG for that matter. Additionally, the scale of visual variety is off the charts. It's a game of worlds within worlds. While VIII and IX were certainly not lacking in varied, memorable environments, FFVII contains more than one can keep track of. Even minor, one-time visit rooms are full of unique details. The cyberpunk-y gloom of Midgar is endlessly appealing, I could bask in it for days. They knew they were doing a once-in-a-lifetime thing and went the extra mile.
Materia- It's a unique way to combine and duplicate abilities, while being limited by equipment grades. It's an extremely elegant yet customisable system, managing to be straightforward and deep at the same time. It's a shame that most of the stuff which lets you get really creative is only available towards the end of the game, but as a system I still don't think they've topped it.
I didn't say this and it's silly of you to suggest it. But up until VII I thought VI was the peak of emotional roller coasters in RPGs. VII goes several steps beyond, and I'm not just talking about 'that moment', but the way the characters reacted to it -immediately and after- was more hard-hitting than anything in VI.
Firstly, I don't consider FFVII to have serious faults. You cite the lack of jobs and reduced equipment types as negatives, but when I play FFVII I tend to give characters roles which benefit from their equipment and stats, no different from any other RPG. Same with battle formation and strategy. Because there are less equipment types to choose from, it doesn't necessarily make it an inferior experience, just a less fragmented one. And if anything, I actually give more thought to equipment in VII than (for example) VI due to Materia slots, XP gain and whatnot. In any other game I'll just pick the equipment with the best stat, but in VII I'll be planning for Materia combos and farming.
Secondly, a masterpiece can have faults. Nothing is 'flawless'.