1. The protagonist can remember their past and it wasn't that bad until the bad guy showed up--this creates actual impetus to seek vengeance on the bad guy without the need to create pointless sub-plots of emotional baggage, possibly involving multiple personalities (Xenogears is a huge offender but FF7 does this as well).
2. The protagonist is not the Chosen One but simply someone who rises to fame and leadership through actual skill and hard work ala Ogre Battle: Person of Lordly Caliber. Also they may actually be LIKABLE PEOPLE in their own right (pretty much everyone in FF6, for example, or Zidane, even though he WAS the Chosen One, though I'm not sure if it actually mattered in the plot at all that this was so).
3. There are no contradictory plot elements, especially ones involving time travel paradoxes ala Tales of Phantasia or even Chrono Trigger
4. People are not asked to blame themselves or God for what is obviously the work of the person asking people to do this (I'm looking at you, FFT), or if this is metaphorical it should be explained in greater detail.
5. When someone kills somebody they are supposed to be loyal to it is for an actual reason which required a hard, life-changing decision, not because they were hypnotized or being impersonated by their evil twin (FFIV and FFXII respectively), or it should be because they are actually evil.
6. Political intrigue is part and parcel of the plot because that's usually pretty fun. There should be at least one evil empire though it should have an actual reason for subjugation other than world domination, at least a reason which is given to the masses, such as religion or racial superiority.
7. The main villain should not turn into a GODBEAST at the end of the game unless it actually makes sense.
8. The main party should not summon a GODBEAST to defeat the enemy GODBEAST unless it actually makes sense.
9. Character deaths should only occur if they make sense within the context of the game. Getting stabbed once when this never kills people makes no sense; getting disintegrated by an overpowering attack or explosion makes a lot more sense. Also, the deaths should actually be important to the plot and pulled of well so they aren't just a plot-device or cheap emotional trick. Also it shouldn't affect the player's gameplay significantly, even if it requires Deus Ex Machina on par with Krile.
10. If your game is tactical character death should never be permanent because it takes for freaking ever to level up those characters (LOOKING AT YOU YOU OGRE BATTLE PERSON OF LORDLY CALIBER AND FINAL FANTASY TACTICS AND FIRE EMBLEM ETC.)
With these ground rules (which can be added) we can start working on our plot.
VS










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