I came up with an idea for a Dark Matter and Shadow Bug mix boss.
The Dark Matter looks like it normally does, but larger and sits on top of body made up of Shadow Bugs forming a cloak like shape, while a majority of them are held together by several stretched out tentacles of Dark Matter. It also has 2 large Dark Matter tentacles that it uses as arms.
HP: High
Attack power: High
It's main attack is to shoot 3 dark lightning bolts down from it's eye, going in the order of left, middle, right, or the opposite. It also sometimes moves it's tentacles up and down (the move so that they can only ever align in the middle) before stopping for 1 second and then will strech out forward quickly, dealing heavy damage but little knockback if make contact with it, or if you are directly hit you'll recieve very high knockback. The shadow bugs also sometimes spawn a random Primid type, but no more than 2 can be on the stage at once. It can also use the tentacles to pound the stage to make shockwaves and as well while trying to crush you. Also, in this battle if your character is K.O'd then Dark Matter will one of it's tentacles to grab it's trophy off screen, and then several shadow bugs will move up the tentacle and swarm the trophy, creating a false character to assist the boss.
If you defeat the false character, it will explode causing the large pile of shadow bugs to fall on top of the boss, stunning it for a short time and leaving the previously defeated character's trophy on the ground, allowing you to either revive the character as an extra stock, or giving you some time to damage the boss easily.
Thanks to God Robert's Cousin for coming up with the whole Dark Matter, Shadow Bug mix thing. I would have included the Phazon in the boss, but I don't know much Metroid Prime. I've never played it.