I completely agree that the Large Missile Slot is the most underwhelming, under-utilized thing in the weapons (even worse than Large Energy, if barely).
I'd welcome any number of power-tools there. A six-shot Pilum; a heavier version of the Annihilator; a Macross-style pod-launcher that was a one-shot area-denial device or death-blow weapon with a nice, slow initial launch and dozens of mini-missles. A bigger Reaper that was one-shot but was basically a nuke with an AOE. Basically, something big, dramatic and interesting; it's a missile slot that isn't common (heck, it's probably the rarest slot in the game, other than Universal) and it deserves some oomph.
A Sabot launcher that actually killed capship shields, even... oh wait, who am I kidding, lol.