I played a bit of every race but focuses on Necrons because I wanted to find a way to play them without starpulse cheese but couldn't; here are my suggestion after my experience of 15+ hours playing necron in 2v2 matches.
Nerf the Starpulse generator by reducing damage by 1/3 and reducing cooldown so it's still a deterrent against ramming and bombers/fighters but not this insane weapon you want to open with.
give Necron ships some sort of regenerating ablative health that absorbs a percentage of damage after armor; Necron ships are too easy to kill outright since they only have armor and a set hp regen that's the same for every ship which long drawn out battles but without shields it's far to easy to cripple and swiftly kill Necron ships if they can't teleport away, which frequently happens if an enemy opens with targeting engines.
remove gauss whip piercing unless in reload stance, since half of your weapons are damaging shields and the other half aren't it makes both ineffective. The reason why Starpulse is so popular to begin with is that Necron ships aren't doing comparable damage to ships with shields.
alternatively reduce the precise trait for necron weapons and double their range with conventional restrictions of inaccuracy.
turn the repair light criticals from a passive to a an order ability like everyone else has (since they have no shields and are always vulnerable to boarding and critical damage) Or give them some means of damage mitigation that reduce criticals crippling their ships since 1 minute is long enough for a lot of damage to be done if a vital system (say engines) are crippled.
Make the resurrection Orb force the equivalent reinforcement order in an AOE instead of just giving 1 crew regardless of size.
Re-implement the Interialess drive either have a smaller cooldown dependent on distance used or use something akin to a combusion gauge so Necron ships can make better use of it to stay out of optimum range of other factions'