I agree that having customisable ship colours a la homeworld is a fantastic idea - but customising the UI with the player's empire colours is asking for migraines. Best thing to do is to make the game as skin-friendly as possible, and before you know it people will be producing star trek skins and what have you.
2 (or maybe even 3) colours for ships is pretty easy to do, (as long as its planned for in the rendering engine - i say 3 colours as you could use RGB channels for each texture to define the mixture of the 3 player chosen colours and their brightness levels). As along as there is also some other way to distinguish whose ships are whose in battle it shouldnt be a problem (because chances are high that some players might pick similar colours). Also, if some bright spark decides to paint their ships black with black highlights, they should still be visible to the enemy
This also brings up another question : player/empire flags. Assuming people want them, there are a couple of possible approaches:
(1) Full colour bitmaps. Simply allow players to use any bitmap (of a predetermined size, say 64x64) they like as a flag. On the plus side, this gives total flexibility. One the downside, well... there's probably always going to be at least one 'special' person in every game who will have a pr0n flag. Sigh...
Also, giving people free reign would mean that many of the non-pr0n flags might just be... rubbish. Kinda destroys the feeling of immersivity IMO if youre fighting tooth and nail for victory against a star spanning empire which has got some cack-handed rendering of their favourite corporate logo or national flag (hmmm... arent those the same thing nowadays?).
(2) Go with something like the Moo3 approach, but *better*. i.e. provide a set of flag shapes, and set the colours based on the player's ship colour choices above. This *doesnt* have to look as rubbish as in Moo3. You could let the players choose up to (say) 3 colours, and use all of them in the flag. Moo3 for some reason chose monochrome flags because they wanted to be able to mess about with transparency - though i cant actually see much use of it in the final game.
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