1. - All ships choose the same Way-point
I don't know how to tell the ships to choose their own way-points and stop being such hogs.
First I thought it was just a matter of maybe putting a For each loop somewhere in there and indeed some of your events didn't look like they were doing the picking quite right, but on further investigation it seems there's something messed up with the RTS behavior. It either just moves the first created object or picks them all it seems in some cases.
One case being doing the action at start of layout:
Recreated it in a simple cap (Start of layout -> RTS move to object Target) and it still only moves 1 instance.
Other than that putting a Delay condition in there seems to break the picking again. It will move all instances... quite annoying.
Well, I hacked your cap a little. Got rid of the Wait object, replaced it with a private variable. Also couldn't use Start of layout for the first move action. That's also fixed by setting that private variable to 0 at start. Guess you'll have to look into it.
2. - The bullets only come from one of the ships
When the bullet shot from the enemy is created, it only comes from the first created ship, not from the one that want's to shoot me.
Can't say I'm an expert for this since I haven't used LOS for anything so far. But what I can tell you is that you should spawn your bullets from the object directly. So don't use System create, but try the Spawn object action of the ship sprite itself.
I changed it a bit accordingly. All of the ships are shooting. But for some reason the LOD seems still off. It seems hardly predictable when ships will actually shoot. Somebody else might know how to handle this better, or maybe I'll find out once I fiddle around with it.
3. - I don't know how to change the angle of the enemy ships when they are going left/right (I.e. player)
How would I get the ships to look left when going left? Or vise-versa?
That one is quite easy. You should check "rotate object" under RTS behavior. Then go down to your object's angles and select N angles. Set the number of angles to 2. Be sure to have auto mirror checked too, and you'll have the plane facing left when going left and right when going right.