My primary suggestion is to remove Hijack from the core gameplay loop.
My alternative suggestion is to make it that the Alien Queen can chose to either commence a Hijack, or to immediately end the game. Both choices would be considered a Xeno Major by the game.
I believe the removal of hijack gameplay would be a net positive improvement to the core gameplay loop of CM-SS13.
As it stands, hijack has virtually no variety in gameplay. Marines will hold the lifeboats. Xenos will attack what is essentially an extended FOB defence. The Marines will either evacuate successfully or all die. The marines may call Distress which will either just be reinforcements for the Marines, or hostile and will either all die, hijack CIC and cancel evac, or meander around till they evacuate after the marines evac/die. Rarely the Marines may defeat the Xenos, but this is merely an extension of the FOB defence, and may often not feel earned.
Furthermore, and a major crux of my argument, I believe the mere presence of hijack gameplay encourages both sides (more so Marines) to conserve their strength during groundside and focus on preparing for the inevitable shipside fight. Why risk losing a lot of marines or material holding a doomed FOB when you can just evacuate and have a better chance of “winning” shipside.
This somewhat also extends to xenos, as they can’t take major risks to “win” groundside because they need every xeno to survive to fight on the Almayer.
No one in the game cares that the xenos technically achieve a “major” or “minor” victory no matter the shipside outcome.
Simply, I think removing hijack would enable both sides to focus 100% of their efforts into fighting the groundside fight. A true slug-fest where you can feel free to sacrifice yourself to achieve victory.
It may also make marine evacuations more, impactful, since the survivors could be given time to actually unwind and roleplay the depressing situation shipside instead of instantly rushing to prepare for the next fight.
As a alternative, let the xeno queen pick to either attack the Almayer or remain groundside. This would let the player have some agency on choosing to keep the round going or just end it.