Sooo...
Unlocking a new fleet gives 2-5 new "ship lines".
ARS give a new ship line, unless you're unlocking a ship that the fleet already has, unless it has 5 ship lines.
Example:
a) I got a fleet, with an "1 assault frigate" ship line (and 3 other ship lines):
I seek an ARS with an "1 assault frigate" unlock. I can do the "grant ship line" action with the fleet, which effectively adds the current number of "assault frigate" fleet line with the ones from the ARS unlock. It also work with "lesser" fleet ships, for example a 40 V-Wing + 37 V-wing unlock brings the total to 77. This action is repeatable if you've got multiple ARS with "compatible" ship lines.
b) If I got a fleet with an "1 assault frigate" ship line (and 4 other ship lines):
I seek an ARS with an "1 assault frigate" unlock. I cannot do the "grant ship line" action, because "there is 5 ship lines on this fleet".
c) I got fleet A with 4 ship lines, including an "assault frigate", and fleet B with 4 ship lines, including an "assault frigate". I cannot give the assault frigate from one to the other, because, I quote: "Can't make this swap, as it would lead to two ship lines of the same type in one of the fleets".
The result of this is that I stopped unlocking ARS if I block a 5th slot, because I think it's better to have larger fleets due to the XP mechanics, and the relative rapid construction of ships (I find myself waiting for metal to come back, rarely for ships to be created). I had a fleet where I had merged 4 ARS into existing ship lines, making it effectively "9 shipline strong". I don't think either of those is good for the game. Even given the random nature of ARS, I think I could reliably have a "11-12 shipline strong" fleet with this mechanic.
I don't care which mechanic you guys find preferable, but, personally, I don't have an issue with having 2 identical ship lines on a fleet, and I'd remove the merging behaviour, and swap restrictions on identical ship lines. I think that having multiple identical ship lines are beneficial because they effectively add to the construction rate, whereas merging slows construction (but, greatly increases the power the the fleet). Also, it's probably been suggested before, but enabling the player to give ship lines to other fleets =) would be great too.
If other modifications for fleet were planned that solved this issue, sorry, didn't know.