Many mercenaries have bad combat roles. Ships with support effects set to escorts, combat ships set to support etc. This changes many of them to either capital or support. I'd have made more capital but I can't get around the rules that small and tiny ships can't be capitals.
Also, Crusade changes weapons a lot and left the old prototype weapons actually useless. Many merc ships that advertised "powerful prototype weapons" actually had the worst weapons. So I changed the power and/or the resource cost of prototypes to try and restore their old role of powerful but inefficient early-mid game weapons.

The Path of Rhuin gets 80 range, shared by the fleet.
The Facade gets Interstellar Sensors.
The Raptor is an interceptor.
Friendly Mike's Traveling Emporium now has a base cost of 500.
The Nail is an assault. Also gets the correct bonus hitpoints that makes it equal to a medium ship.
The Sabre is an assault. Also has +50% beam range as stated instead of of +100%
The Bludgeon is an assault.
The Fist of the Setting Suns is a capital.
The Elembrial is a capital.
The Sussinkt now has a base cost of 1100.
The Retribution is a capital. Gives a 50% bonus to fleet beam range and beam accuracy instead of a flat 0.5 bonus. Jamming bonus reduced to 25%.
Hivebase One is support.
The Viper is a capital.
The Bitte is support.
Safety In Numbers is support.
The Heptium is support.
The Gestalt is support.
The Scow no longer gives fleet wide jamming. Only to itself.
The Erragis is a capital. Also it gives its kinetic damage resistance to the whole fleet as stated in its description.
The Sidrat is support.
The Compact is support and now has a base cost of 2300
The Straisor is support.
The Lutitia is support.
The Linked Aerie is support.
The Excruciator is a capital. Also it gets an attack and defense bonus of 25% instead of a flat 0.25 bonus.
The Fissure is a capital. Also gets the logistics reduction it was missing, and an attack bonus of 25% instead of a flat 0.25 bonus.
The Sickle gets an attack, range, and move bonus of 25% instead of a flat 0.25 bonus.
The Collective is a capital. Also gets an attack bonus of 25% instead of a flat 0.25 bonus.
The Helmder is a capital. Also its jamming bonus goes to the whole fleet as stated in its description.
The Shaout gets an attack bonus of 50% instead of a flat 0.5 bonus.
The Hermitage get and attack bonus of 25% instead of a flat 0.25 bonus.
The Cixma is a capital.
The Wraith an attack bonus of 25% instead of a flat 0.25 bonus.
The Pewpewpewpew gets the 100 bonus hitpoints stated in its description.
The Praxis gives only 1 ideology point per battle.

The Pollen and The Perseverance each have only one colony module now. With two colony modules they cost two administration and held extra population that wouldn't even fit on a new colony.

Changed just about all the threat/fortitude/value settings to improve AI ship roles in general.
I removed the prototype weapons from the tech tree. It was too hard to balance them for multiple purposes. If I made them too good they'd be overpowered for standard designs. Not good enough and mercenaries wouldn't be worth buying. Now there's government ships too that use them and they can't serve three masters. So they're gone from standard ships, they're used on government and mercenary ships, however any mercenary ship that advertises "powerful" or "prototype" weapons gets double fire rate on those weapons. This should keep mercenaries useful without overpowering government ships and not overcrowd the tech tree with weapons.