Needing one sci, one eng, one tac, one cruiser, one sci ship, one escort will not eliminate cheese, but will limit the amount to which it can be applied, and make it much easier to counter.
For example, with the makeup above the cruiser is the only ship that can make effective use of FAW, but can be countered by a single target weapon subsystems. FAW stacking is no longer an issue.
Likewise, only one person can use scramble 3 per team, and because you have fewer people the scramble is much easier to clear.
So if you decide to make teams strictly balanced with one of each ship class and one of each career you really don't need the white-list on items or powers (although I agree with the scorpion fighter ban). It takes care of itself. Having both class/career restrictions and a whitelist feels like it is both restrictive and redundant.
The reverse is also true, you could cut out the ship class and career requirements and keep the whitelist. This would allow everyone to form any kind of team, but would dictate how the individual team members need to play.
The big issue with specific ship classes here is the Klingon faction, and of course the BoP which can really fit any role. If you want to keep the class/career restriction, I would add two more categories so you have Escort, Cruiser, Sci ship, Carrier, BoP, where you can only have one of each on a team. It might be wise to lump carriers in with sci ships to limit sci spam, and you could also conceivably lump in BoPs with Escorts. If you can only have one carrier on each three man team the pets aren't as much of an issue. Don't forget that on the fed side you could have an MVAM/Galaxy-R/Vulcan team open up with five pets as well.
Personally, I like the idea of having force-ably balanced teams with only one person allowed per ship class and career. It will lower the amount of possible participants, but will create interesting strategy. You could conceivably walk the middle line and simply not allow all three people to be in the same ship class or career, which would mostly limit cheese but allow most people to form teams and participate.
Lastly, I'm not crazy on the idea of free agents being tied to particular teams once they fill in. The original picture I has was the free agents would roam between teams and form their own teams and fight each other, as well as do exhibition matches against premade teams and other teams of free agents -- that it would be a fun way to meet new people and fleets and share knowledge. There is significant advantage if you want to have set class/career requirements that free agents be able to fill in where they are needed when they are needed.
I would agree with the gist of this. If you can only have one of every ship class and one of every career type, you limit the "cheese" option notably - and sufficiently. And I would make a place for BoPs and Carriers as well.
On the KDF side, I would say that they should pick from this list:
BoP, Carrier or Fleet Support Vessel
Escort or BoP
Cruiser / Battlecruiser
With additional restriction of only one BoP.
If it later proves problematic that people use, say, the Bird of Prey and a Raptor both in an Escort role to have "unfair" DPS, or combine a Fleet Support Vessel and a BoP to have "unfair" science abilities, that could be adjusted accordingly.
Starting to sound better (quite a bit better actually), although I fear you still might run into issues with the format. One issue in particular now stands out to me:
If you can only have one of each ship class and one of each career option, yet you are only allowed one substitute per team you run into an obvious problem. Because of restrictions, there's a very good (about 2/3) chance that if one player cannot make a match the substitute will not be able to fill in anyway since he will not be qualified as per the regulations. There needs to be a loosening somewhere, such as in the number of allowed named substitutes, flexibility of rescheduling, or perhaps in the "free agent" system to make replacements easier to get on a team. I'm sure there are a few solutions with various pros and cons, and one or more of them needs to be included to fix what seems to be a fatal flaw.
Taking the suggestions you have presented .. the regulations have been softened on free agent accessability and team compositionwith cross faction teaming it will be easier to fill in with free agents.
Thank youe all for the great feed back... It will make this a great succes
The limit of subs is now to two... I want to be able to include as many people as possible. Every registered player in a team or acting as a free agent Can play as any of their VA alts on the same account.