I agree with the suggestion for making automatic fleet formation optional, as well as for automatic fleet formation to only occur at the final destination rather than when flight paths cross and two ships end up on the same tile in the same turn.
In a similar vein, I would suggest that non-fleeted ships and understrength fleets stacked in the same tile should be treated as a fleet (up to the logistics limit) for the purpose of defending against attacks made by another player, so as to avoid having stacks of 20 individual fighters that take 20 move actions to kill just because they're not in the same fleet.