That would be really great Rammastardock. Now I am excited to hear what the team respond like.

It would be very rare for two players to choose the same colors and icons so that it was impossible to tell them apart with basically the entire spectrum that the human eye can see to choose from in RGB. In the event that two similar colors were chosen the icon  above their planets/ships etc would tell them apart them. 

It is more likely that if the player that was not given freedom to play with any colors would more likely not be able to reserve their favourite colours. I imagine that the lobby is currently setup to make sure no two players are allowed the same colors? EDIT: Checked and the AI at least does alter itself if you choose the same colors

Sometimes in Dawn of War especially because it was 40k where the player could literally choose any color, people chose the same default space marine chapter colors out of a tonne of preset lore chapters. It was never really a problem. A little confusing when the AI chose the same chapters but never caused major issues. I mean consider that a civil war has two sides with exactly the same uniforms and colors except for their symbols. In DOW/HW it you'd also see people sometimes choose the same color for each model section making a jet black or other such solid color. A ship of shiny obsidian if you will. Most prefer a contrast though. They can then make star wars ships or star trek ships etc Whatever their hearts desire to role play. 

I should add that a lot of games allow you to choose the AIs colors anyways if it's an issue. But it was only ever an issue in dawn of war when you wanted to play against space marine chapters wanted to be the enemy and so being able to choose enemy AI chapter colors was good.

In Homeworld it never mattered either. Just so rare with people choosing such a huge range of RGB palette colors. 

Perhaps leave the default colors as they are and then have a button to "paint/create" your own colors which can be host server globally disabled for all. But I suspect this option will never get used unless in super serious rules based tournaments. 

I love naming my ships and planets and colors and icons customisation is a step further to that. It has been done before by other very successful games. People love to paint things.

Another point at the moment would be that the two stripe colors you do have do not make a difference to some components which are always the base color. So if somebody were to paint their ship black in order to make them hard to see you would still be able to see the base colors, apart from the icons above their heads.

Even if two players intentionally chose the same colors it would not be a huge problem as they would likely be on the same side. In any event hovering over ships tells you whose they are. 

If it is was ever percieved as a problem the games host would just politely ask somebody to change colors before starting the game.

P.S. Nebulous Fleet Command which is currently in alpha also does this with no issues. Incidentally each ship can be named like in sins which is nice.

18 seconds in this video shows this, they even have the ship name on the side of the ship. Which I would not expect in Sins2:

Volt I hear you, but at the same time I don't think any problem identifying your fleet/culture/planet via color here is far outwieghed by the players having fun making their faction up with their colors. Colors, symbols and of course your portrait are a major way people identify with their faction... for the next 3-5hrs of play it takes for a sins game to finish. Or over multiple games. Plenty of games do it and I list another one below, stellaris. Although I think in stellaris is not a prime example as its space battles are just blobs and I think the color choices are really more for the faction backdrop. The biggest difference between sins and stellaris is that space battles in stellaris are litterally just blobs going at it. The cool thing about stellaris is that you can build your ships and equip weapons according to your best choice to beat what the enemy has. This is one thing that could be interesting in sins, remove the cannons on a TEC frigate and replace them with lasers because you are primarily facing X enemy atm.

Heck I would go so far as letting the player write lore for their faction and have other players able to discover and read that lore during the game.

Stellaris has 72 colors to choose from for each of it's two color choices iirc
12:30

Irony is that now we are told we have less cartoonish colors and some people of course want the brighter ones back.

This was solved by an adjustable brightness meter in dawn of war one’s painter. 

Once again I would humbly suggest letting people choose their own colors and brightness from a pallete rather than controlling  presets.