To be honest, the fact that the darkest black on Smoke palette made some abilities invisible was a saving grace for me - it's so useful on Protea (first ability, especially the shield-giving mode), Frost (Snowglobe and Avalanche), Gyre (I want to see the warframe, not a ball of tiring, blinding ball of energy, please), Ember (Sudden blinding with fourth ability when too many enemies are around, second ability on self etc), Duplex Bond for sentinels and so much more... I'd say it's best to either give us some kind of "color intensity" option, like with sigils, or add a "new color: transparent/invisible". For the perfect white and this invisible black Smoke palette was worth it, after all...
Whatever the choice would be, I'd love to have an option for an "invisible" color, be it with perfect black right now, or something else.