Not sure if this is broken or working as intended, but it looks like auto-assign refuses to assign talentless officers to ships. I have ships without commanders (cheap pickets that only require R1) and commanders without assignment, and the auto-assign now button doesn't change this. I suspect that if the "score" for the commander taking up the assignment is zero, i.e. if the training rating is 0, then the commander isn't assigned.
That is working as intended. I didn't want talentless officers taking up a post for a whole tour when new officers might be more suitable.
Aha! Not a high priority request, but could you make this an optional behavior? I like to stick talentless officers (especially those with good Governor skills) in a command slot to give them the opportunity to acquire on-the-job training and become talented.
I've also found that I've been overriding the auto-assign (which I love, btw) for important command slots like warships or ground unit HQ. If a new-construction cruiser comes along, I'll look for a DD commander to promote (who's more talented than the auto-assign), even if his or her tour isn't over. I'll then promote someone else into the DD hole, etc. One advantage to this is to breaks up the huge "start time + 2 years" cohort of tour expirations present at start-up.
One side effect of disallowing talented commanders that I think I've noticed (at least early on) - freighters soak up all the talented officers in the initial assingments at startup, so new warship construction ends up without a commander (hence my promotion strategy). This isn't a big deal for me, but here are some ideas if you want to use them:
1) Have a "garbage scow" checkbox for each class on the F5 screen that allows talentless officers to be assigned (or you could just use the existing "conscript crew" flag)
2) Have a numerical rating for each class that is set on the F5 screen that indicates the prestige of the command. A very talented officer in a low-prestige command would be considered (possibly with a "breaking tour" penalty) for higher-prestige commands when they come available. this is essentially what I'm doing by hand. For example, the score of an officer in a command could be multiplied by (1 - prestige_difference/higher_prestige) to represent breaking tour, which would disallow purely horizontal "promotions". This could also be extended to staff positions, a lot of which are irrelevant (fighter ops for logistics command?) but are still sucking up highly qualified officers.
Like I said, though, I'm fine if you don't do any of this.
John