Ruckdog, my assumption would be that there are point values assigned to the models, and you would still agree to a specific point value for the game with your opponent. But you would be free to achieve that point value however you see fit. If you wanted to run 25 frigates, or 5 battlecruisers/battlecarriers (or whatever the big ships will be), that would be up to you. But then you would be limited tactically in what you could do. (And this is all just conjecture on my part).
That being said, economics and model availability may also help determine what players field. For example, if the game is only available in box sets for the first 12 months or so, it might be hard to get your hands on 5 battlecarriers without having to buy 5 boxed sets and getting a slew of other ships you didn't necessarily want. So I think most people will likely still play with small, medium, and large class ships.
One question I have is the number of factions. In the video/pc games, the only "factions" were the UNSC, the Covenenant, and the Flood. And the Flood was really only encountered on the Halo rings themselves, although they did manage to hijack a Covenenant ship (cruiser, I believe) in Halo 3. So I wonder if we'll eventually see Flood-infected ships (both human and alien) as a third faction in the space game.
For the ground game, which I assume will come after the fleet game is out, having the Flood as a third faction would be interesting. Another idea, for the ground game at least, would be to have a separatist human faction. The SPARTAN program was designed to quell separatist rebellions on distant human-colonized planets. So, if you wanted to play the game in a "vacuum" (i.e. not following the storyline of the Halo universe at all), you could have Flood fighting human separatists, etc.
One thing I hope they do NOT do is bring the Forerunners in. While they are part of the Halo universe, I think they all died out millenia before the events of the first game.
Do we want to take bets on how long it will be before we see someone who has built at least a portion of a Halo ring structure as a backdrop for their fleet game??
Please pardon my Halo geek-out moment.