I think somebody mentioned something like that in another thread already, but I find it deserves its own thread:
It would be great if we could set preferences for the defenses that automatically assembled ships get equipped with. In the moment as far as I know that is only determined by "BestDefense" or so in the XML files, and what is your best defense depends solely on the techs you have researched.
But most of the time I need other defenses than those that I researched most. So if we could set preferences like "60% beam defense, 20% missile defense, 20% kinetic defense" or "0% beam defense, 100% missile defense, 0% kinetic defense" it would make life a lot easier, because right know you have to design your own ships when you need something other than automatically generated, and self designed ship designs are not automatically upgraded, so you have to do that yourself also, what is a lot of work ...
I would be content if that was a global setting that affects all shipyards, but even better would it be if you could set the preferences for each shipyard individually, since on large maps it's not uncommon that you have to fight several enemies at the same time with different ship layouts.