After finally coming across a rather complete set of the Epic:40K rules (the third edition of Epic, which shares a lot with BFG in terms of rules mechanics), I was quite taken with how they treat titans in the turn sequence.
Each player's army has a strategy rating. The player with the higher strategy rating gets 3 tokens and the lower rating 2. The tokens go into a cup or some such device allowing blind choice. The first phase of the game is players alternating declaring flyer missions (starting with the lower strategy rating): player A declares first mission, player B second mission, player A third mission etc..
The second phase of the game is movement: the player whose token is taken out of the cup may choose to move all their units before or after the opponent (and we note that because there are only 4 tokens left, one player's chances of choosing to go first in the next phase are increased).
The third phase is non-titan shooting. The player whose token is chosen may choose to fire with one of their formations, then the other player chooses one and shooting continues to alternate between the two until all normal things have fired. A player may always choose to skip firing until later, if they wish.
The fourth phase is titan (and other war engine) shooting and the initiative is determined again! The player with the initiative again chooses a titan to shoot with, and titan shooting alternates between players.
The fifth phase is the assault phase, and the initiative is determined again, with players alternating to move and assault with formations. After this phase is the end phase and then the turn starts again.
If I was to do this for BFG, I would probably have an Ordnance phase at the start (ordnance actions alternating like flyer missions) and another one at the end of the turn (once again alternating).
The second phase I might have capital ships (or maybe just battleships?) move first with initiative chosen by counter, with a second movement phase for escorts (with initiative again chosen by counter). I think alternating between players for each ship or squadron would work well here too.
The fourth phase (after ordnance 1 and 2 movement phases) would be determine initiative by counter and alternate firing escorts, followed by a second phase of initiate and capital ship firepower. Maybe the escorts and capital ships would be swapped, or maybe all ships and squadrons would be in the same phase?
After shooting is done, I would have a second Ordnance phase before the end phase. I'm not sure when ordnance would be launched, maybe in the first phase or maybe in the shooting phase?
Of course, either Tim's or Gun_wun's suggestions for determining the order of shooting could be used instead of the counter (though I like how the counters give some more predictability without making it certain). Gun_wun makes a good point about low leadership being a big penalty, but Tim makes a good point about leadership giving a very tangible advantage! Though maybe with alternating activation Tim's suggestion wouldn't be quite so harsh?
Some food for thought, anyways!
Though I must say, I don't mind the current system too much... it always makes the ships seem appropriately ponderous! Though I would be in favour of trying my suggested modified Epic:40K system as a replacement because separating the escorts from the capitals keeps some of the ponderous feeling (whilst alternating activations perhaps help with multiplayer games and boredom between turns).
Thinking Stone