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Important information as a result of this feedback (lots of merged threads):
Right to the meat - we are reverting the Emissive Energy inheriting Secondary energy as of next Hotfix. The reason we added this was because we read player feedback indicating disappointment 'Secondary Energy' did nothing on the Warframe itself, so we tried to give it meaning. And now the meaning has swung too far the other way!
You can expect a way more in-depth colour customization to come soon - at least we're experimenting with something really wild. We will be working on giving you (Forma using players) even more options - 4 energy customization slots total. Primary and Secondary for the Warframe itself. Primary and Secondary for the Warframe's Abilities and Effects. This means your all-Red Ember could have Blue Fire. Your Green Saryn could have Orange Spores, etc. But - it's in the laboratory. Stay tuned for a Dev Workshop as we work on this. And if you don't use Forma, you won't be forced to. Your Secondary slots would just be the same as Primary, so nothing would force a Forma, etc.