I think the question of whether or not traditional writing "rules" (and as an aside I care little for traditional "rules" in artistic domains) apply to video games is still open. It goes without saying that an interactive medium is very different from a non-interactive one, probably in ways that hardly anyone has theorized yet.

That said, some of Renmiri's specific points are still worth replying to, though WK has done a good job with several of them:

Quote Originally Posted by Renmiri
1) We are never told why Vaan tags along with Ashe, why Basch fiercely protects Dalmasca, what resistance leaqder is Ashe that doesn't even know her uncle is on her side, etc..
2) A complete stranger to the plot is introduced and never mentioned again (Havharro, Miguelo, Drace...)
3) A protagonist is not the leader yet is the main "action" character (Vaan)
4) Several plot twists that "redraw" the story
5) Clichee: Mean cartoonish villain (Vayne), Mad scientist (Dr. Cid)
6) Clichee: Dumb sidekick (Bergan), Evil twin (Gabi)....
7) Unnecessary, meaningless blood spilling (Resistance ships, almost Rabanastre)
8) Ambiguous morals (Occuria are jerks, Dr. Cid is a bad guy but his plight is sympathetic)
1) is pretty much a video game staple, and there seems little reason to single out FFXII for it. There's nothing remotely plausible about a blitzball playing 17 year old with an outfit that looks like it was rejected from Kefka's wardrobe being accepted as a guardian and then embarking on a world spanning and world saving quest. I don't care what in-game reason is provided for this - it amounts to little more than an excuse for continuing with the JRPG cliche of teenage world-saving heroes that's no more believable than the motivations assigned to Vaan or Basch.

You concede that 8) is not a rule, but inexplicably claim that the writers left it up for you to make the blacks and whites "grays" when IMO the "grays" are obvious.
I don't see why 2) is a big deal at all in any story, though I think Drace was another example of wasted potential. But other than that I don't find anything disruptive or confusing about her or Miguelo. In Miguelo's case the fact that he has no role after the opening is understandable, and Drace was just underdeveloped. Like WK I don't remember Havharro at all despite just finishing my second playthrough.
WK also points out that 4) is a defining feature of JRPGs, and I don't see at all why FFXII handles it less well than any other JRPG. FFIX and Chrono Cross are textbook examples of games that handle plot-redrawing twists poorly, and indeed FFXII refeshingly lacks "ZOMG EVERTHING YOU KNOW IS WRONG!1!!!11" type plot-twists.
3) I don't see how Vaan is the "action character" after the first third of the game.
5) A cartoonish villain is not a cliche as far as I can tell, but just a general weakness in itself. Nevertheless you have yet to give a convincing argument that Vayne is cartoonish, you just assert that he is. IMO he is far and away the least cartoonish FF villain yet, and only a few stupid lines delivered during the battle with his Novus form qualify as cheesy. Overall, he's much less embarrassing than anything else the series has produced thus far. Cid does adhere to the mad scientist cliche all too often, but still strikes me as relatively well done. Bergan is not dumb, he is simply authoritarian and is in any case not a sidekick.
7) Doom 3's plot has unnecessary bloodletting. By comparison, what is meaningless about the destruction of the resistance ships? Since when is "almost bloodletting" bloodletting? You write:

Quote Originally Posted by Renmiri
Last time I checked we had no Aeons here The attack on Mt. Bur-Omisace's refugee camp was completely unnecessary to the plot, as were the "mommy, talk to me mommy" heartbreaking NPC dialogs there. It spoiled my enjoyment of that portion of the game, particularly because it is never addressed at the end. Ashe and Larsa never sent relief supplies or anything. Another plot string left untied, raised for the sheer heck of it then abandoned

X had a much darker, bloodier plot. Continuous genocide for 1,000 years ? A land of widows and orphans ? Yet we get to DO something against it and the entire sunny cheery landscape distracts you from the horrible reality the world of Spira faces. On XII the genocide seems like an after thought that no one, not even you, should care about.
The attack on Bur-Omisace's refugee camp was pretty minor really, and not out of character for Bergan. It certainly doesn't qualify as "genocide" (probably Sin's killings don't technically qualify as genocide either). Sin's killings also aren't continuous, and IMO their impact is diminished by the fact that they are thwarted over and over in an almost mechanical fashion. So what if he rises up every ten years to wreak some havoc? He's guaranteed to be destroyed again anyway. Not only that, but by simply defying a tradition the characters find out that killing this almighty monster is rather straightforward in reality. I felt that the whole Yu Yevon/Sin summoning was not very well explained either. It may be that I wasn't paying close enough attention, but why was the whole convulted set-up with the final summoning really necessary for Yu Yevon's continued existence? What does this stupid tick/squid/spider thing do all day anyway?