As someone already mentioned prelates, I guess I don’t have to do other than keep this portion as reminder of their existence.
What other I mention is that I doubt it would make the story impossible, it’s true that Elites & Brutes are physically more imposing than humans yes, but physical prowess is only part of what makes a species succesfull, in this case in battle.
Brutes surely are already something that shouldn’t be taken head on lightly, much less so in “super” form, however, I see Brutes as being far too hotheaded for their own health & usually that type of temper easily gets one killed when air is filled with lead. So I doubt a simple program would provide them means of becoming something that is absolutely impossible to stop.
And while I see elites being as more prominent candidates for difficult opponent if received augmentations, they too have their, imperfections.
A warrior species, already partly equivalent to most SPARTANs with their current technology.
So what would they lack then in the battlefield then? Their morality is possibly their limitation, their own type of honor code their tripping stone, while human soldier does whatever is necessary to win, high ranking Elites give opponents chances in battle to experience a “fair” fight, as much as one can be arranged, many also possess arrogance, akin to Ripa which also turned to its downfall in the end.
But in the end, everyone is a different individual. Some supersoldier Elites or Brutes would prevail over some SPARTANs while others wouldn’t.
But what I see as inherent edge humanity has in Halo universe is their craftiness, ability to adjust to & survive situations where survival could be deemed impossible by some standards.
So while some species in Halo have some strongsuits that can be more easily perceived visually, humanity in Halo universe has their strongsuits too.
Which is why I don’t believe that even in supersoldier form, other Halo species would absolutely dominate humanity critically more than it does currently.
And more importantly, humanity has survived covenant fleets which were the biggest killers in modern era of Halo, so I doubt few landdwellers would change the odds of humanity surviving that much either.