After finishing the coretech warehouse quest (for coretech), and having previously done the Rathound King quest, I think I see a pattern where allies are too fragile for combat.
During the Rathound King quest, I reloaded about a dozen times to try to save Edgar. Killing the king on my first turn on multiple attempts couldn't save him. And he wouldn't move whether he got entangled or not, guaranteeing death from the ancient rathound.
Similarly, stupid AI makes allies suicidal in the warehouse fight. Henderson (a sniper) charged into melee range on more than one reload, guaranteeing she'd either get smashed with a hammer or one-hit killed by an enemy sniper. And there were a lot of other problems with that fight.
While it would be ideal to make NPC AI much smarter, it would be easy to increase armor/damage thresholds and health. Honestly, even with smarter AI, allies could probably use a buff.
Also: how about allowing at least one "free" friendly hit before aggro? I'm fine with the way that friendly fire discourages certain tactics, but it's a bummer to have to reload because a 90% to hit attack goes wrong. Isn't it enough "punishment" to deplete the health of the already fragile allies? It also seems unfair because I've seen enemies screw up grenade throws without starting to fight each other. Actually, I'd settle for enemies fighting among themselves, though I'd prefer more forgiving allies.