Honestly... And I know I'm weird... I'm against this.
As an experienced pilot, if I ready up with an AI slot on my crew, I am readying up knowing that I risk getting another gunner or pilot, or even an engineer who only wants to shoot guns. If I am not comfortable with this scenario, I will leave and find a new lobby with people who are willing to wait for me to get a full crew. Otherwise, I will customize my ship to handle the possibility of having the less than optimal crew and see what I can do.
Flying organized experienced crews alongside organized ships is going to hand you a victory unless you are facing similarly organized and experienced opponents. This can be fun, but nowhere near as fun as taking a late join second pilot, sticking them on one of your guns, and carrying a helpless teammate to a 5-4 victory. After the match, talk to your crew about how they should try to only join as engineer then switch accordingly. If I ready up, I am accepting the challenge to carry an interesting crew to victory.
For less experienced pilots... this will do at least 2 things.
It will teach them to not ready up with AI, nor to pester people to ready up with AI.
They may eke out one of those special wins where they know they shouldn't have pulled through. The best way to get hooked on a game like this is to have those victories.
I cannot vouch for what this may do to newcomers to the game. It may be that the current joining system keeps our numbers low, and your proposed change would boost the number of players who stick around. But there is an upside to the current system that you shouldn't overlook. I am not saying that your opinion is wrong, simply pointing out that it isn't all downside. It just makes things interesting.