This article interested me, because it echoed many of the thoughts I'd had on, of all things, Final Fantasy VIII. Yeah, that one. The middle child in the PSX FF brethren, doomed to never quite receive the attention of his younger, thicker sibling (VII) or his mightier, more respectable elder (IX).
VIII, like AITD is riddled with bad design decisions, yet each one redeems itself on reflection by being a good, swift kick to the face of convention. The worst issues that plague JRPGs are all swept away by a new and radically different 'Junction' system. Gone is the ability to simply grind your way to victory, mashing attack and intermittently casting some Cure spell (a la VII) - enemies don't just level alongside you, but ahead of you, gaining significantly better stat boosts. Fighting need not be about gaining experience, but there's now a more varied, more interesting incentive to go out and fight, which is to draw spells and obtain a collection of items. GFs shook up a stale and predictable battle system that had stayed virtually unchanged since the days of the very first FF.
Of course, that doesn't stop them from still being bad decisions. Giving any player equipped with more brain power than a cephalopod to junction himself to 9999 HP and max stats in the first few hours of the game was never going to turn out well. Nor was building a junction system that punished magic casting use with stat decay: in essence, players had little incentive to do anything other than junction to Str and spam attack, or, failing that, junction to Mag and spam the GF command command instead, the latter being only marginally more relentlessly uninteresting than the first. Hunting down rare enemies to obtain some obscure item vital to a weapon upgrade became tiring quickly, and the card game was either a pointless distraction or an express route to 99 hero drinks, that then made the game virtually un-losable.
At least the spirit was there, though, and perhaps with better execution and a little more thought, FF as a series could have taken a radically different direction. As happened, though, the cool reaction from fandom prompted the self-consciously conservative IX and may well have seeded the stagnation JRPGs have suffered from (and for) over the last decade.