I like to imagine that after the whole fiasco with augmentations on the S-IIs and then the S-IIIs (mostly the twos) the higher ups didn't look too kindly on augmentation. So who cares really? They're Spartans, regardless of if they have unbreakable bones or steroids running through their system. The only thing the S-IVs need to improve on is their armor now. The fact that the MJOLNIR Gen 2 Armor gives them the strength to break an Elite's neck is also pretty badass, remember the whole point of the augmentations in the first place was because the armor was impossible to wear, after the war and collecting Covenant samples of their armor they probably picked up some tricks to not have to augment themselves.