The "outsourcing" of the boss fight is just that they asked the people who made their AI middleware to program the boss fights because they were rushing to release the game. (Source: I know someone who worked for the very small company that made the AI middleware) That's also why so many areas are so small and why the boss characters aren't properly introduced.
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.
I always felt the boss fights were so out of place in DX3 and one cannot solve the game without killing unlike Deus Ex 1 were it is possible to play through without killing a single person!
