As shields take damage, there should be an increasing chance that weapon hits pierce them. Once shields have reached 100% damage, they disappear entirely
nope, the entire opposite

Shields get STRONGER as they get damaged (YES!!!)
Ships with knocked out engines that are very close to planets and stars should be at risk of falling into them
not possible. I already asked.
Engines, the bridge and other modules should be targetable
certain modules (unknown which) are on the biggest of ships. nothing on smaller ships (frigs on down)
Ships with knocked out Bridges should maneuver randomly and be at risk of collision.
doubtable.
Ships/planets/stars should be as close to scale as possible without losing playability. It is a hard balance to manage, but I would rather the designers err on the side of 'Bigger and more Realistic'.
they've already adressed this. any bigger and the gameplay slows down dramatically, halting the game.
Fleet Orders while in Phase Space
asked, and currently unknown.
but your logic doesnt make much sense, because you could just send a message thru phasespace.
Also, it will prevent elite players from permanently bouncing huge rapid reaction fleets around in the void between their systems
AM regen will stop this. also will allow limited bottlenecks (because your enemy wont be able to pierce right on thru all of your planets on one tank of AM gas)
Also, asteroids, planets and stars should help hide ships from sensor detection if they are located behind them.
nope.
although you can hide them if your foe isnt paying attention (much like you can sneak up on somebody from their front if they aren't paying attention)
Anti Sensors: Devices that mess with sensor info should also play a part. Effectiveness of these Anti Sensors should be determined by tech level, range and the tech level of the oppositions sensors.
nope.
sensors are always in the gravity well of the planet, outside that there isnt anything to see. you cannot see into gravity wells that you do not occupy (i.e. if you dont have a ship at that planet, you dont see anything)
-EMP type weapons: I believe that there is already some kind of disabling/energy draining weapon similar to the EMP from the Homeworld series. If not, then one should be included.
unknown. but its probably somebody's special ability (TEC?)
Allies: Allies should be able to share sensor information and donate/use each others ships.
not sure about ship donating, but sharing does not occur. sensors are probably shared, but thats speculation.
Gravity Well Projectors: I hope all races can build these devices to prevent/delay Phase space escape. Maybe some of the races might be able to build better ones than others.
Vasari has a special ability blocking phase escape. but who knows for the rest.
-Cloaking/Ramming/Capturing: I hope ships with these abilities can be built into the game
Possible/Unlikely/No
I think ramming has been denied (but there should at least be contact damage) cloaking is in the wind.