If only I had time to think about this right now!!!
(Just thinking out loud here - sorry if I'm stating the obvious)
A Command Ship has specialised functionality that provides superior command and control abilities to the guy (or gal) in charge. These facilities can take up a significant amount of room and resources, which in turn can have an adverse impact on the capabilities of the host vessel (especially if it is a retrofitted capability). This means that the Command Ship either has to be bigger (to include the specialist features as well as normal features) or a trade of is imposed and the ship is actually less capable than its comparable sister classes.
So a dedicated Command Cruiser could be less capable (offensively anyway) than a normal cruiser, think of it as a science ship in some respects. A Command Cruiser should have good defensive capability and should have enough features to make it something to defend and useful, for example a superior sensor range than may be expected.
I'd also suggest (if things like this were possible) actual command based "specials", e.g. telling all ships to "Fire Now," or "Fire on my target" or "Pick random targets" or "Formate on Me" - actually making the Command Ship part of the command interface (and thus really giving incentive to protect it!). I'm not brilliantly familiar with FlOps capabilities... guess I'll have to install it and give it another whirl at some point.
Unfortunately I don't think many of those ideas are possible in fleet ops. It does just work on an dll expanded version of the A2 engine. They have only been able to do what they have done thanks to exploits in the original Armada 2 engine and exe.
Still I have thought of such ideas as sensor blocking (originally in the A2-YY it was to be a simple sensor jammer ship) and a beefed up version of the stock frigate.
Now as for changing the role to something else... I've forgotten what the classes and roles are, can you (re)post them please so I can get a wider appreciation for how a new cruiser type could fit? (Or point at the relevant post.)
I do like the idea of the repair shuttles though.
Sure mate, here is a list and description of the fleet set-up.
[fieldset=Fleet listing]
(SC) Scout
Basic long-range scouting vessel. Used to explore unexplored space and observe enemy actions. Only equipped with basic shielding and energy weapons. Scouts have long range sensors, allowing for extended line of sight. Often scouts are re-purposed science ships or destroyers/frigates.
(FF) Frigate
Basic starting unit combat ship. Only combat ship buildable at the start of the game. Frigates are small ships built on a destroyer frame but not as capable as destroyer. They are often either a old destroyer or a purposely build unit such as a prototype destroyer class that has been supplanted by more capable designs. Best utilised in early game as a spam unit for early raiding.
(DD) Destroyer
Destroyers come in various configurations, most factions utilise at least 3 destroyer class vessels. Designed as early front line combat ships and later support/escort vessels for cruisers. Specialised destroyers are also present within particular faction fleets. Included are heavy destroyers that focus on damage and AWAC destroyers designed for extended sensor range for example.
(CL) Cruiser
Medium sized vessels, the cruisers have multiple purposed depending on faction and design, larger and more capable than destroyers, Some destroyers have multiple variants designed for different duties. Included is an AWAC's cruiser to supplant the destroyer of a similar purpose, combat cruiser, troop vessel, assault craft (such as fighter carrier). Most cruisers fill in the support role often supporting the larger heavy cruisers.
(CA) Heavy Cruiser
Main fighting vessel in late game. The heavy cruisers make up the bulk of a players fleet. Usually quite well at offense and defense, depending on the faction.
(CC) Command Cruiser
Support cruiser, the command cruiser is usually an experimental design, often build for fleet support and give a bonus to nearby ally units. Different factions have different uses for the command cruiser. Depending on a factions ideals, it could be a passive repair ability, an increase in offensive capabilities or a full support role and not ideally suited for combat. Often considered to the battlecruiser what the support cruisers are to the heavy cruisers.
(BC) Battlecruiser
An unscaled heavy cruiser, the battlecruiser is stronger than any heavy cruiser. More expensive too.
(DN) Dreadnaught
Designed as a weapon of war, best way to describe a dreadnaught is a starbase killer. Dreadnaughts are purely designed to inflect damage. While slow and powerful they are not as durable as a battleship. Often best used in siege groups.
(BB) Battleship
Well rounded heavy combat unit. While the dreadnaught focuses on plain damage even at it's own expense, the battleship is more equal in it's offensive and defensive values. Considered a flagship of any taskforce, the battleship is almost as strong as a starbase and many have called them starbase with nacelles. Very few are in operation by any government due to how expensive they cost to build and operate.[/fieldset]