I'd try to keep it as simple as possible.
You'd take all the ships that can fly solo and designate them something.
You'd take all the ships that can command a fleet or fly solo and designate them something else.
You'd take the ships that can fly in a fleet (but not solo) and designate them something else, if they exist.
And that'd be about it, unless you want to do PF and Fighter CnC.
To be clear, this is just a renaming of existing non-restricted ships. Let's try this as an example.
The first ships (solo only) would be called STRIKE ships, and have that designated. Therefore, you would have FFS, DDS, CAS, BCS, DNS, CVS, and so on, appending whatever else you want afterwards to designate it's particular type. A solo drone cruiser would then be CASD.
The second ships are COMMAND ships, and would have that listed, meaning FFC, DDC, CAC, BCC, DNC, CVC, and so on.
The last ships are ESCORTS, and are thus called FFE, DDE, CAE, BCE, DNE, CVE and so on.
Now, this dosen't do anything to controling or policing CnC that Cleaven has brought up, and is a legitimate concern.
However, it makes it blindingly obvious to anyone who reads the CnC rule which ships can be combined with which. xxSx must fly alone, xxCx may have another ship, and xxEx must have a xxCx around with them. Secondly, anyone who reads this rule can quickly see if anyone else is following the rule or not, which may not be immediately obvious otherwise.
This may grate on a lot of people that want 'correct' tags, but this won't bother me much.