Kieve or Karto did some testing awhile back- we found that shields capped at 5 layers. Hmm.
Was this before AE? Because I've tried ships with up to 7 layers of shields.
Not only do they block missiles (1 damage each missile) they are also shown on the UI the same way the 5th layer does, except over the other two bubbles.
The only real issue with them was that the system itself beyond 10 health bars would be damaged and require repairs every time you reloaded a save game or encountered a ship that would have them (which should be rare. That Mantis Teleporter Barge at Sector 4 was fixed).
In fact my latest ship, the Zoltan Magistrate uses this or can use this [/toots horn]
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On another note: There is an unused song called Federation that comes with every FTL soundtrack.
https://www.youtube.com/watch?v=ezUAozazL8M
Is it a possibility to have the song used in Federation sectors?