I think some things are hard-coded to the AE-enabled button; such as stun. You can see the stun disappear from weapons (in the hanger) when turning AE off, but there are no extra blueprints to override the weapons.
From the little testing I have done:
I think artillery systems that don't have a weapon assigned cause the game to crash. These don't seem to default to ARTILLERY_FED.

(Test: Tried loading my ship, Bahamut, game crashes when trying to select it.)
Reactors above the normal limit crash the game when entering ion storms. (Test: My OP Testrel has extra power, and it couldn't enter an ion storm. Game auto-saves now, so progress isn't lost. Sorry, Potential. It seems your days might be numbered.)
Medbay and Clone Bay are hard-coded together. Assigning them to different rooms doesn't allow you to have both. When you change systems, it seems to retain the system level from the other system. You can assign two systems to the same room (I don't think that is new), but I never saw what happens when that room takes damage.
Unassigned systems still show up in stores.
Level 10 shields still work. I didn't try any graphic changes, and the 5th level overlaps the 1st level on the shield indicator at the top.
Slugs don't detect red dots anymore. You can see what race is in the dark rooms now.
Glows have changed. I don't know much about this yet.
Door and Sensor stations default to slot 0, direction UP.
Anti-Bio Beam has a color tag for changing the beam color.
Graphics for 2 weapon slots and 4 drone slots.

None of the new ships use these. Will they work?
AE has a system repair bomb. Bug fixed? Hope so... I wanted to include system repair on my purple Crystal Harmony Bomb.
I may have forgotten some things...
