you can change the color of clothing, but colors are faction specific. The "stealthy" ability of the Operative is disguising as the enemy, and since you take on his clothing and physique when you do this, it doesn't matter what you wear. And for the last time, there are no ninjas or assassins - there is an Operative, who main use is for recon and sabotage.
Really if you want to make a assassin, just make a soldier with light physique.
Anywho, I'd like lots of balaclavas, bandanas (lots of "a"s
) and the black hoodie and ill be set, and maybe an easter egg from fallout for the heavy dudes...a power armor suit?