Why not have it so that no more than 3 ships on either side are legendary ships. You make them extremely expensive compared to their standard counterparts, per class hull.
OR
You could always revive and adopt the old ship assignment system, in where a ship of a certain class or type is assigned to you, but in this case, you're assigned legendary ships. Each time a particular ship is given an upgrade, such as the CA to the CAR or what not, for example, have at least one legendary ship for that new upgrade.
If this has already been suggested in here, then forgive me. After the last post on the first page, it was hard to keep track of for me.