Putting your fleet in-between but not on/around the shard i think may part of your issue. the best way in AI to have a large prolonged fleet engagement imo is to over-saturate the AI target list making it waste fire on non critical targets(low mark fleet ships for example) while you the player can focus critical targets more efficiently. Group/ formation move is pretty useful.
Also unless your difficulty is particularly high the 3rd to 5th city shard is a reasonable point to consider significant warhead usage. By that point if you have been clearing for lvl 2 cities some single digit AIP warheads don't mean much any more. Armored warheads are of particular note because they start from the highest hp and go down therefore munching star-ships, guardians, and dire guardians first.
Consider that Each city lvl 2 city is a best case of 60 aip(target system plus minimum 2 adjacent). 5*60=300 aip from cleared systems alone in best case(unlikely even on x maps). Maybe a few systems less depending on layout. Add in the K requirements for Galactic capital level stuff, 30k or 10 normal planets worth, on top off whatever K you needed/used before. FS beyond a certain stage leaves normal aip behind and never looks back. When you reach that stage use everything. AIP be damned.
