I think I see this as more a matter of personal preference rather than an objective flaw. I mean, the very annoyingness of Trance helps tie in in with storytelling, and FF9's battle system is a lot more tied to the story than usual.
Sometimes being annoyed by a game isn't a bad thing, it means you value the times when everything works out.
I also think my definition of an average gamer is a little different. Mine is one that will look into the system, learn a few tricks, but won't have the patience to obsessively refine or play cards with every single NPC, where grinding is a means to an end (ie. to get powerful enough to defeat that particular boss) rather than an end in itself -there's no actual need in game to get any character
anywhere close to level 99, or draw 99 of every magic, or any of the things you really need to break the system. They don't just happen by chance.
Incidentally, 3rd tier magic isn't game breaking in FF8, it's the rarer spells like Aura and Meltdown that are true game breakers, which are pretty hard to find if you don't know already.