It seems to me that the main reason for the oddness and un-Deus Ex-ness of the boss fights is actually because the three Tyrant boss fights, and to an extent th

It seems to me that the main reason for the oddness and un-Deus Ex-ness of the boss fights is actually because the three Tyrant boss fights, and to an extent the Three Little Tyrants themselves, are really modelled on Metal Gear Solid, not Deus Ex. Start with a motley crew of freakish mercenary antagonists; let the player catch glimpses of them in cut-scenes; then properly introduce each one in a boss fight in a traditional sealed boss arena, making the player fear and empathise with the boss as the beautiful doomed monster he or she is before killing them, thus ending each chapter on a note of melancholy and settling doom. Oh, and also chaff grenades are key to beating them easily.