Hmm, I agree. But a rule which says 'always take weapons damage, never shield or engines' isn't a totally 'fair' tradeoff - a ship could, if rolling damage checks, take damage in several at once. It also begs the question of whether a flotilla with one 'weapons bank' could be in bad shape under this rule, which one with the same points cost but two banks could be in better shape, since MC's rules assume we're using bank-specific damage.
Would the following rule work: "Flotillas, when damaged, never take shield or engine damage, but take two weapon damage results and roll as normal for special systems."
As long as every flotilla was required to have three or four banks, that would work very well (damage check one: two banks damaged, or one bank completely destroyed. Damage check two: all four banks damaged, or two banks destroyed).
It would also work well with Murtalianconfederacy's rules for how many ships and of what type they are, since those rules give some good ideas on how to set up the banks based on what kind of ships are in the flotilla.
Here's a sample flotilla from an IP we all basically understand:
(33) X-Wing Squadron -class Flotilla Nova TL: 2
Armor: 1 * 1 * 1
Hull: 1 * 1 * 1
Thrust: 12 8 6 4 3
Shields: 5 6 6 6 6
ECM: 0 0 0 0 0
Weapons: 0 1 2 3 4
[V]: 1x Red Leader and Red 1 (Dfs/Pnp) / [FH] / 1 - 2 - 3 / AD: 1 1 1 0 0 0 0 0 0 0 0 0
Mode2 (Gid/Skr/Slw) / 2 - 4 - 6 / AD: 1 1 1 0 0 0 0 0 0 0 0 0
[W]: 1x Red 2 and Red 3 (Dfs/Pnp) / [FH] / 1 - 2 - 3 / AD: 1 1 1 0 0 0 0 0 0 0 0 0
Mode2 (Gid/Skr/Slw/Dx2) / 1 - 2 - 3 / AD: 1 1 1 0 0 0 0 0 0 0 0 0
[X]: 1x Red 4 and Red 5 (Dfs/Pnp) / [FH] / 1 - 2 - 3 / AD: 1 1 1 0 0 0 0 0 0 0 0 0
Mode2 (Gid/Skr/Slw) / 2 - 4 - 6 / AD: 2 1 1 1 1 0 0 0 0 0 0 0
Special: Hyperdrive
Under the proposed damage rules, on its first damage check, two 'vessels' from the flotilla are gone and one 'bank' is destroyed (oh no! We lost Red 4 and Red 5!) or two 'vessels' from the flotilla are gone and two banks are firing at a -1 (Red 3 and Red 5 are both gone!). If you get unlucky and roll for damage, the whole flotilla can't go to hyperspace - maybe a destroyed ship had the coordinates, a damaged ship's debris are causing interference, who knows.