I have noticed that it gets complained about a lot when someone is up against tyranids or spacemarines and that is that that no one thinks it's balanced that their fleet can just be one hit KO'd when they have few ways of retaliating other than stay at a distance which is rarely an option for anyone who aren't eldar. the quickfix solution the devs have is to just make boarding capable vessels be expensive as heck. but this seems to create other issues for these boarding heavy factions.
my suggestion is that boarding be changed so that it doesn't act like a button you click to have the crew of a ship vanish from reality in a millisecond, but rather make it so that when a vessel is boarded it starts loosing it's crew over time proportionally to the troop damage dealt. this gives other fleets the opportunity to retaliate before their ships are de-crewed and it just generally makes more sense for battles inside the ships to take time from a realism perspective.