Something that bugs me is aliance/morality stasis.
As an example:
I've been laying SW:TOR recently, and when I arrived on Alderaan, I learnt that there is a civil war between the various noble houses, with House Organa supporting the Good/Republic side.
Because of course, if Princess Leia's adopted family is good, then all their ancestors 1000 years must also be good.
On top of that, I later discovered (via a lore unlock) that House Organa have basically been The Good Nobles for thousands of years, ever since Alderaan was first settled.
Now that is longer than most real-world nations have existed, or even civilizations. The idea that one nation/clan/family would consistently be "they good guys" for even a fraction of that time is absurd.
It would be nice, for once, to have a setting where - when the story revisits a setting a few hundred years later - we find that, for example, the "good church" has become corrupted and /or schismed; the noble houses have merged/split/etc so that the current heroes are decended from earlier villains, the militant order of religious fanatics have calmed down and become a harmless charity/social club/etc; the orc ravening hordes have established a nation that is no better or worse than any other kingdom, and enjoys just as good/bad relations with them as they do with each other; etc.