Taking over ships will be done in FPS mode, every man for himself. Defenders will have time to place turrets, breach doors and put other defense mechanisms. Attackers will have short time frame to breach and take over command room. There will projectile, melee and energy weapons. At least that's what they promised.
In singleplayer most likely there will be pure FPS missions, where you need to infiltrate in some base, free someone, steal something. Dunno about multiplayer, it would be awesome if you could pull out a gun in a bar full of players