The Flagship section is already the single most powerful section. For the humans at least, there is no section stronger than it weapons-wise save maybe Projectors due to the nature of those weapons, and no section save Shields that provides a better defense.
This is taken direct from the Rorschach wiki:
Flagship section: 18000 HP, 18 small, 6 medium, 5 large, 8 beam mounts.
Armada CnC: 10000 HP, 18 small, 8 medium, 1 large mount. (no contest)
Armor section: 12000 HP, 10 small, 12 medium, 3 large mounts. (weaker in every way save medium mounts)
Barrage section: 13000 HP, 0 small, 6 medium, 4 large(missile only), 3 torpedo, 8 beam mounts. (close, but missile-only mounts limit usefulness)
Blazer section: 12000 HP, 0 small, 6 medium, 0 large, 11 beam mounts (no contest, 5 large turrets vs 3 extra beams)
Heavy COL: 12000 HP, 4 small, 6 medium, 4 large, 3 COL mounts (may be stronger in alphastrike with proper COLs, but reload's too long)
War section: 7000 HP (WHAT?), 6 small, 0 medium, 5 large, 8 beam mounts (you frikkin kidding me?)
Projector section: 12000 HP, 10 small, 12 medium, 0 large, 3 projector mounts (5 large and 8 beam mounts for 3 projectors and 6 mediums... questionable trade, otherwise neat)
There's also speed differences of course (CnC are usually slower), but those are mostly natural. After all, you don't want your flagship to be the damage soak for the enemy's first attack, right?
So, there you have it. The Flagship has the most CPs of every other command option in the game, and considerably more firepower and armor to boot. Not quite a battlestar yet (that honor goes to the Morrigi flagship, which also mounts a wing of drones), but already quite formidable. Now couple this with the Electronic Warfare command section...