Recently switched difficulty to Endless with 5 IA on a medium galaxy to get more challenge unfortunately Vodyani are too strong when they get a good start and unfortunately IA is currently unable to upgrade weapons.

However, in the late game arround turn 100 the Lumeris started building Line ships and I found them pretty hard to get down.

Even with 18 command points shared by (2 x crusader + 1 x brand + 3 x grouge) with up to date lvl 3 weapons you just get owned by a non upgraded Line ship. I tried different combos with rockets and beams to max the damage at different ranges but I'm still unable to get a single Line ship down with 18 command points.

The Line ships I'm talking about had 2576 dmg / 5950 HP

Another issue I started facing with big space battles is you can't arrange fleets like you would like to. That would be nice to be able to select where you want your ships to locate among the 3 attacking lines. 

I had the same issue with a Sophon carrier. I had three fully upgraded Craver Carriers and I couldn't put much of a dent in it no matter what weapon combinations I tried. It seemed like they had buffed up armor or shielding. Maybe endless difficulty buffs the AI's ship defenses?