Even in the first Deus Ex, the game's tone shifts hard from espionage to comic-book superhero genre about halfway through, with the Dentons and Simons having DC super-hero levels of power imbalance, supported by the enemy grunts' vocalisations as they shit themselves. But the presence of the heavy bots and commando suits is sufficient to clarify that the augmented agents only have a power-balance shifting advantage as agents. In straight combat, there's plenty of other, cheaper, more reliable, options. My impression was that a large part of the Denton project (and its referred to as an aim in the context of the 'Men in Black') was that a key part of their advantage was that they were supposed to be 100% loyal due to being controlled from inception onwards. If augmentation was simply 'more powerful all round', there'd be no reason for the bots and the commando suits to exist alongside the mechanically augmented agents.