I can see the point on the similarity of cannons to railguns as I can't think of a railgun as much else besides a cannon, but not necessarily plasma/missile or wave/beam.
Just judging by what the terms bring to mind on a whim a wave as opposed to a beam would be a <) shaped "projectile" that expands (and weakens in intensity) over distance. With that I can see creating weapons for slicing ships in half, dismembering turrets. Like taking an axe to them instead of a spear point. That's a use. The shape of the wave weapon could be defined by its secondary. Say a wide circular AOE pattern and high damage and reload from a pulse as opposed to a narrow crescent and longer reach from a beam. Thin, weaker waves in quick succession from cannons. Missile -> extremely wide crescent, covering 45* in front of the weapon, oriented vertically but narrow horizontally. A battleaxe for dismembering an opponent.
You can turn plasma into a DOT projectile weapon which disrupts waves (and waves cancel out incoming plasma spheres (Has anyone tried using missile spam to defend against high-yield cannon shots yet? I coulda sworn intercepting a missile likewise destroys the cannon round, although it's quite hard to tell.)). Using it with push/pull/stop and EMP effects gives you a way to lock down a target with a quick shot that spreads its effect out over a few seconds, instead of dumping it in the instant and letting them recover. A plasma/missile could be used to affect armor in an expanding radius around a point of impact (very good for making wide holes your bombers and missiles can exploit!) while a plasma-pulse burns deep into a target over the course of its duration.
We DO have more than four options here, guys. Use yer imaginations, dammit.
I would really like to see this flak weapon come to pass, actually.