I am glad there will be something to replace the automated fire, because as said above already, it is absolutely mandatory in dealing with swarms of facs, and I guess now also fighters.
I had specific designs created with only one fire control (since auto-fire only ever utilized one), that I set out to deal with this. (in the Astral Republic thread the very first thing was such a situation: fighting dozens of swarm facs + mothership in a nebula via complete automation)
On more than one occasion I actually just used my beam fighters to harass on some of the ai's quite sizable civil fleets. Clicking through 20-50 uninteresting civil targets is just not the job of the admiral..., and it takes long enough watching it play out even with the automation still.