As I understand it, the Helminth system was proposed as a way to bring older frames and underutilized frames back into the limelight and give them the ability to swap out bits of their kit for something that holds up better.
I've done it a few times meself.
The problem that I've seen, is that people went the opposite direction with it like they always do, the little number crunching goobers. Helminth is used to infuse that one piece of universally beloved kit from underused warframes and slap it into their god tier creations, widening the power gap considerably.
And while that genie's now out of the bottle, I have a proposition that could make Helminth a lot more useful to grind for and stock up with, in a way that would I feel help bring Helminth closer to it's stated goal.
I feel like this is the one area where Destiny outshines Warframe at the moment- allowing the players to swap out their character class on a moment's notice, that changes things from how any or all of their abilities work including altering their super.
Right now, we have these mod cards that take up a slot in our loadouts and tweak the Warframe's abilities as part of the Syndicate system. Excalibur for example, has his Chromatic Blade Augment, which you get for maxing out with Steel Meridian. It's a very useful mod that can help Excalibur hold up pretty well to near any faction in the game.
What if, instead of these mod cards, they instead became recipe cards or infusions that you got from the syndicates to install in Helminth?
Instead of Helminth being able to graft new abilities from other warframes into each other (initially), it can swap between the augments for the players needs?
(The Helminth exclusive abilities could still be swapped in as they do now, and then Warframe specific abilities could be a higher ranked perk of leveling Helminth, say rank 10)
Each time I subsume a frame into Helminth, it absorbs the frame utterly, and would allow me to feed it Augment recipes for later use with that specific frame
(Naturally, I could toss in augment recipes ahead of time as well.)
as an example
I take my Mirage out for a spin, but before I start the mission, I swing by the Helminth chair to swap out her Prism for the Prism Guard version instead, while also swapping her legerdemain for the Explosive Legerdemain version. I feed Helminth their juice and cookie for the initial augment, and then that ability is tweaked, and can be swapped out in the chair at will from then on.
I decide to run Ember in some high level content, and make sure to tweak her Fire Blast to the Purifying Flames version to ward off status ailments in higher level content.
Including a system like I propose into Helminth would still allow the player to use the Syndicate system as intended, and also allow lesser used warframes the chance to come back out into common use once more, and could even allow some flexibility in play styles within a single Warframe to suit everyone.
Summary- Give Helminth the ability to let frames swap between their ability augments as a kind of subclass system, and only at higher ranks with Helminth would the player be able to swap in other Warframe abilities. This encourages players to find out all the upswings of a given frame, While not taking anything away from the Syndicate system, at the same time enriching what the Helminth can offer players who use it.