You've got some decent ideas. I think this is a good one, for instance (it can be very hard to tell, at a glance, which of your weapons have been knocked out of commission):
It also would be a good idea to make weapons permentally destroyed or out of ammo turn RED, while temporarily disabled weapons or reloading ones appear yellow/orange.
These are interesting possibilities as well:
Purple Nebula: This is a flux-charged nebula, when entering it your flux steadily rises at a constant rate. They also block vision into it, but not out of it.
Blue Nebula: This is a flux-draining nebula, when entering it your ship loses flux at a steady rate. They block vision into it and lower the sight of ships in it.
Electromagnetic Storm: This is a special dust cloud that fires out electricity. When inside the storm your shields don't work, when nearby but not inside one it might shoot you with a lightning bolt that shortly overloads your ship.
This, however, is remarkably rude and presumptuous:
Developers aren't perfect, they make mistakes. They can't catch anything, nor can they think of all the wonderful possibilities that everyone else can.
In a different context, that wouldn't be so bad, but in this context—you just tried to completely redesign their game for them! You're calling them out on "mistakes" that don't exist, or treating features and planned features as if they were mistakes. You propose space monsters, a pirate society, and an inter-factional war as though there weren't already an elaborate backstory in place (which has been in the works for years, I believe). You propose gameplay and graphical choices (no restrictions on weapon types, the ability to play the game from a completely zoomed-out perspective) they've explicitly said they don't want as features. You've asked for things that are already in the game (e.g. graphical indicators of damaged armor) or that are obviously planned (it should be entirely obvious that 200 FP is the intended cap for fleet size in the campaign right now).
And jeez, before you complain too much about the difficulty, you might want to practice a little more. The autopilot should not autoperform you, and losing one or two ships from your fleet should not be a crushing blow (nor should it happen very often).