What you're wanting is just broken. There would have to be far more restrictions on how the Warframe's abilities can be selected for it to even begin being balanced.
An ability could only be chosen in the 'slot' that it takes from the existing frame, so you couldn't put Roar and Eclipse on them at the same time because they're both Rhino's and Mirage's 3rd skill. Or that you have to use at least one of the Helminth exclusive skills such as Golden Instinct. Or that they have their own set of skills based around supplementing the skills you choose from other Warframes, etc etc.
If you want to have a Warframe based around the Helminth system then maybe still create a unique Warframe with their own set of skills, but have their passive be that they bypass the 'diminished' aspect of skills. Maybe link the ability to select a second helminth skill to the 3 Warframe boosts available each week. I don't know, it'd all be messy.