Actually, I think rather than toning down big fleets in power, those skill limits (at least in case of some skills) force fleet diversification.
For example, Carrier Group skill gives you maximum bonus at 8 fighter bays in fleet. Phase Corps gives you max bonus at 30 or less recovery points of all phase ships in fleet.
This means that in order to take full advantage of the skill bonuses, it's optimal to have a mixed fleet of warships, carriers and phase ships. Putting all eggs in one basket makes the bonus weaker, but spreading them across ship types has lesser impact even in case of a big fleet.
@EDIT: Come to think of it, I really don't like the idea. Having freedom to choose whatever playstyle I prefer was a nice thing, and now those limits basically take that away by forcing me to pick a little bit of everything.