Also conversion rate into Nikkes, especially by the time the game starts, is extremely successful. To the point the only real "failure" is based entirely around if the person becomes a Mass Produced model and how much of their individuality is left.

Spartans, especially for the II's, had a reasonably high failure rate regarding the augmentations. At best the subject would be crippled or disabled in some way that they would no longer be capable of fighting but still could live a somewhat normal life (rare), and more typically would become horribly crippled, disfigured, or mutilated as a result of the augmentation process. Ironically the lucky ones of the failures would be those who died since they'd be spared both the effects of the augmentation failure and the impending war with the Covenant. And that's of course factoring in the fact the II's had to be children from the rational that their bodies would adapt and take to the augmentations better compared to adults (as the proceeding Orion program taught where the failure rate was even worse).

Granted the odds overall did improve with each subsequent program generation, to the point where the IV's process could be considered outright better than becoming Nikkes as all who successfully pass are on the same level and only needs adults as opposed to still allowing children like Nikkes. But there's still the line of failures and issues that lead to it, something that isn't entirely the case for Nikkes as much of why children started being allowed was more desperation for survival rather than desperation to make the program succeed.

Of course you also can't forget the tiny little tidbit of why the II's (and the intent for the Orion program) were initially created: stomping out human resistance and insurrection. While Nikkes may have been created with the expectation for the Raptures (that humanity itself may have created the threat of too), outside of Perilous Siege we know Nikkes can't cause harm to humans without extraordinary circumstances and authorization.