As a new player. I'd like to weigh in a bit on this. Personally I have definitely had a fair bit of difficulty distinguishing friend from foe, however, I think Helmic makes a great point.
the confusion over whether someone's friend or foe means someone needs to whip out their spyglass and use that zoom to let the pilot know.
I think that increased usefulness to spyglasses is great.
The issue in my opinion, isn't really a matter of determining friend from foe. You have ways to ensure the target is correct. By using the spyglass, or popping up the minimap real quick.
But when I look at that image that Jazzza posted. I'm instantly struck with a sense of confusion. The fact that the red and blue are equally prominent in the colouring of that ship, actually leads me personally to believe that the ship belongs to some faction that has both red and blue as it's colours. Being new, I wouldn't really know better.
Alternatively, how would I know that the blue are the flags, and the red are fins? I could just as easily see the flags as some kind of sails, and the fins as the team colouring. But in the heat of the battle, I'm probably not going to think that deeply, and I don't think a game should be designed in such a way that requires that in this sort of situation.
To bring this into context though. People will learn, I'll learn, and if an alternative method of creating good aesthetics can't be found, then I guess life will go on.
However, I think there are ways that could comprise both good aesthetics and more clear team colouring for that ship. For example, the goldfish can still be given colour without it having to be red. Making all the red become blue is clearly not a good solution, but the red could become more of an orange or a brown (though brown is a bit dull), or a burgundy to make it more distinct from the team colour red. Or alternatively if red wasn't one of the team colours then it wouldn't be an issue. You could also go with something completely different like purple or yellow. But I'm not sure if that would look good.