I like the idea that every ship gets an initiative stat (one that uses the fleet initiative as a base and then adjusts it based on how nimble the ship is supposed to be). How hard would it be to roll a die and leave it next to every ship to represent said ship's turn in the game? Only in cases of ties can the player decide which goes first.
Now, if you have 2 Hyperions, 1 Omega, 1 Oracle and 2 Hermes, you roll 1 die per ship and hope for the best: Obviously the Omega would have the worst initiative of the bunch so perhaps you would roll their initiative, add the race's base INT (EA has a +1) and then add a ship modifier (for the Omega, it would be something like a -2). I would believe that most ships, like the Hyperions and Oracle, would have no INT modifier and the Hermes, being a tiny and agile ship, would get a small bonus (like another +1). So, if you rolled a 3, 5 for the Hyperions, 2 for the Omega, 6 for the Oracle and 1, 5 for the Hermes, there would be a net INT for each ship: Hyperion ships would be at a net 4, 6, the Omega would be at 1, the Oracle would be at 6 and the Hermes would be at 3 and 7. In effect, your opponent would know that the order of your movements (not necessarily your shooting) would be the Omega, Hermes, Hyperion, Hyperion/ Oracle (then the other one), and finally the Hermes.
You could always create clauses that nothing can go below 0 so that there would be no worry about negative numbers. Finally, squadrons would have to use the worst initiative of the ship.
Finally, this would create a new and interesting critical effect as well. As a base, use the speed reductions to also effect their initiative (with Adrift as setting the net INT of a ship to 0).
For those who thinks that this is too much book keeping or too much math, I have tested something very similar for a different game system (one that never got published). The system seems very complicated if you do all the work, write it down on paper or try to keep it in your head. The system is very quick if you just leave the net INT total as dice, next to each ship and then remove the dice as they move (respectively).
The only downer to this scenario is that the Omega will rarely, if ever, getting a shot off with it's boresight. So, adjustments would have to be made to specific ships too.