I think an Ewar officer station and skill can be interesting.  Even maybe have modules that give Ewar benefits for the entire fleet, to allow for Ewar dedicated ships.

Not sure if this has been reported yet? When a jump point stabilization module is combined with a tractor beam on the same ship, the ship will not do the jump point stabilize function.
Is this intentional? 

This suggestion is something that I've been thinking about since the way I play my game I tend to award medals outside of the current conditions.

Such as:
1. Medals (up to 3 different grades) for being assigned as CO of a major fleet vessel.
2. Medals (up to 2 different grades) for being assigned as Flag officer on a Flag deck.
3. Medals (A lot of different ones) for being assigned to different Admin commands - This one, I was thinking, when the admin command is selected can we set upon the officer being assigned to this command they receive the allocated medal (selectable by a drop-down box or some such to indicate what medal)? I actually have medals for Combat, logistics, survey and such.
4. Yearly randomly allocated medals. - Ok this one is a lot tougher as what I tend to do is pretend that there's a yearly competition for my navy and the combat admins (warships) and civilian admins (cargo and such) will get a medal.
5. Medals (up to 2 different grades) for being in a combat zone. - This one is like that of the US army Infantry combat badge.

The first and second options should be trackable since the officer history can track when they are assigned as commanding officers and/or flag officers.

For the 3rd one, I've already suggested a method to assign the medal.

For the 4th and 5th options is a lot harder to think of a method to assign those.

Does anyone have any other suggestions?

What I'm asking for really is a way for us to add additional conditions to the game without direct input from Steve adding it himself.

Seems like a flat buff doesn't really have any of the nuance you claim it does.

I'm not sure how you get that from what I've said.