second, on the wave cannons. consider that wave cannons are inherently more effective than any other weapon system due to the damage-armor type tables. upgrades to this type of damage are more or less already passively boosted by a decent amount against most targets. the skarovas are so powerful that upgrading their weapons becomes worthwhile in almost every circumstance where you can afford it. at that stage of the game you're not really going to be able to find a more potent damage upgrade (provided you've already got as much missile upgrade as possible). also noteworthy is that 3 of the cap ships have significant wave cannon batteries. the Devastator has basically all 3 types of weapons (4 missile launchers, 2 particle beams, 4 wave cannons). The whale is mostly wave cannons, i think its primary weapon system is 6 wave cannons. the marauder also uses wave cannons as its main weapon, though admittedly the ships strength is not direct combat. really its a pretty good upgrade for every cap ship except the Desolator (which uses almost entirely its missiles and is rarely in range of any of its other weapon systems) and the Carrier (which is both rarely in range and lightly armed in general).
The Skarovas and Jarrasul are the only ships that use Wave as their main weapon. The Devastator uses Pulse Beams as it's main weapons, with Phase Missiles and Wave Cannons being secondary front-firing weapons. The Marauder, Carrier, and Desolator all have Wave Cannons, but they play the role of minor side-mounted weapons with Phase Missiles and Pulse Beams being the main frontal firepower on all three ships. The Karrastra Destructor also has side-mounted Wave Cannons, but you never want to get siege frigates into a fight anyway.
Basically, it comes down to the fact that Wave weapons are exclusive, expensive boosts for the Skarovas Enforcer, just like Plasma is to the Destra Crusader. Heavy Cruisers, with their strength, make the player pour tons of cash and resources into upgrading their special Composite weapons. Good for the TEC, their Kodiak doesn't suffer from this problem.
Phase Missiles - Anti-Shield
Wave Cannons - Anti-Armor
Pulse Guns - Cheap but weak
Pulse Beams - Simple raw firepower