I think Halo's later campaigns proved how it's preferable not to have boss battles. I'd rather have epic, unfolding battles--you push forward, they fall back, etc.
Boss battles are pretty much dependent on "I am Big Bad staying pretty still so the player can shoot me at various times". It just doesn't fit as organically to story progression in my mind. Can you make it work? Sure. But it's a spice that's best used sparingly.
Boss fight Idea:
Chief and a squad of allies advance through a large squad linearly in progressively harder stages. A little bit like the Ring hall in Halo 3 where arbriter 'silences' the prophet. In every stage there is one bigger boss character who falls back to the next stage as his troops are killed. You can kill the boss character at any stage if you are skilled enough, and his troops will react accordingly (like grunts do when their elite dies). if, on the other hand, your allies all die and it becomes impossible to advance, you do a one on one fight with the boss character inside a ring like the brute boss in Halo 3.
But the crux of this will be the epic music an pacing set by our mystery, non-Marty composer.
Or chief can crawl into a vent, silently use his non lethal dart gun to remove the guards, drag their bodies back into the vents, disable the cameras and hack the computer that enables the nerve gass in the boss hall. If he has enough praxis kits, obviously.