not sure about their lore, but i think the "weakness to magic" might work for them (that trait is currently not used by any of the premade factions, anyway). an ophidian/naja themed 1 point trait would be cool, though (replacing stealthy)

+1. I like the ophidan/naja idea too, though vulnerable to magic works too.

So what did get fixed exactly?

Was the trait removed (which?) or was a weakness added?

They probably got rid of Assassin's Tools.

According to the .91 changelog- Umber loses the Stealth faction trait and gains Warriors

Does that resolve the issue they have too many faction points?

Indeed

This is what I've tried to do with my custom builds, but doing so tends to make some races weaker due to the disparity between some of the traits.

Still have issues with the class choices made by AI sovereigns. Built a custom Yithril sov, with no magic traits, set up to be a real bruiser. Encountered him later in game, he'd chosen the Mage path; his only spells were from Aeromancy, at 15th level. Same game, encountered a sov set up to be a mage, with 2 magic traits, of course, she was an Assassin.

The traits assigned to the AI also need more transparency, why do traits such as Expansive/Proud/Militaristic get assigned as they do currently, and is there a way to determine how they are assigned via starting sovereign or faction trait selection?

i also wonder what the idea behind their default sovereign is. he has some melee oriented abilites, which suggests the probably should be played as an assassin or warrior, but on the other hand he's a beastmaster, which pretty much makes path of the mage mandatory if you want to tame some of the higher level critters (for the extra spell mastery from the prodigy traits - which also opens some nice synergy with his death spellbooks [almost irresistiible wither/curse/mass curse/blind to support his pets] ). 

Well if maybe Warriors could instead unlock Leatherarmor there would be no problems. And the trait would even be good.