I will use Trooper armour as an example for this suggestion as that's what I have the most experience in using, heh. My suggestion follows along similar lines as the current mod system, just with 2-3 extra slots which will affect the appearance of the armour itself.
The 3 mods will cover the armour style, colour pattern and colour theme for a set of appearance customisable armour (This feature could be purely for future sets of armour, much like how set-bonuses in mods is only for current new gear). With each new set of armour released there will be a base style, which will be fairly minimal in detail (Heavy armour shows plates for protection etc, but no asymmetric extra plate like on the War Hero set).
Currently I have though up of 3 style mods that will add to the appearance of the armour. One set around elegant/ornamental/formal dress/honour guard style which will make any piece it is placed in that little bit flashy (Pipping around edges, showing medals, stylised shoulder armour), another set around rugged/scout/well travelled that will give armour a look that it's used and practical (Survival pouches, weather protection, knife pouches) and finally another set to make armour more menacing/defensive (Extra plating like the asymmetrical shoulders on War Hero set, Spikes, Trophies)
Finally the last 2 mods will affect the colour pattern and actual colours of the armour.
This would allow people to pick and choose to a style they like but the actual armour base itself should be recognisable.