It's an RPG dude. Story is NOT something you can dispense with. Dialogue, yes. "Plot" as it were, sure. But a major component of an RPG's gameplay is the progression of the story. These are characters meant to associate with the player. The story is meant to carry the player through sequence after sequence. When a game up and discards the story, especially in a genre where story is important, it has failed as a game. It's one of the major items which distinguishes an adventure game from an RPG, and even in the adventure genre, what SO3 did would be nigh unforgivable. Maybe you like to be more forgiving, but I don't.
Many of the oldest RPGs pretty much phoned in stories and/or left it to the imagination of players, so that's a bullshit argument. Even if you argue the angle of people making their own stories and playing them out that's only a portion of the players rather than the collective whole, nevermind those who DO skip past all the story these days anyway, even for RPGs. Frankly, it's not as if there's any one thing that MUST be universal beyond being entertaining (or being able to get SOMETHING out of it anyway) for video games, it's your own hang up if you call an RPG a "failure" because of its story in spite of how good its gameplay is, that sounds more like the game fails to meet YOUR definition of an RPG rather than whether it was actually a good game or not. Though to be fair it probably does say something about how much you enjoyed the gameplay if you allow a weak story to invalidate that, plus it's a fair point if a game focuses on cutscenes far too much and even makes them unskippable, but SO3 was only really problematic there for the first few hours, and as I recall is largely innocent of the latter unlike some games I'll hold a bad story against more (NiGHTS!)
Let's not forget the battle system was bug-ridden, plonked you down on a boring mudball for half the experience, had some of the most illogical world construction (HI THERE 5-MINUTE-APART-CITIES), and it featured shit like Farleen. I don't care if that was "good VA", the choice was fucking stupid.
Some of this, on the other hand, I think is fairer. Bugs are more objective, though how easy it is to forgive them is dependent on severity. The occasional graphical glitch isn't a big deal, and in a massive and sprawling game world it's to be expected if some issues arise, but crashes in something like SO3 ARE pretty lame. I was luckier there though, and the one crash I had I forgave for hilarious timing (right at the start of the final fight).