[Suicide Junkie]

Well, at best you will get the AI to randomly use them.
Requiring AI compatibility kills a lot of good ideas.

The Neural Combat Net does the best experience thing, but if you can train one ship up, you can train them all.

Now, you could simply make the NCN smaller and easier to use... combine that with reduced training rates & maximums.
Given those changes, you will end up with combat veterans being spread out to "command" their own fleets. Of course, only humans can do that.

Another good way is to have oversized command ship hulls. This would be something extra large so it carries lots of cool stuff, but by using mounts and hull-based maintenance reduction, you can make it take a long time to build (but still be reasonably cheap to maintain)
You end up with a few big powerful superships, and lots of cheap cannon fodder to protect them.

Some mods also go with special bridge components, which will increase or decrease maintenance costs while providing combat bonuses or penalties.