They kind of had to do alien Nazis because that's how "Zero Hour" ended.
Well...by default I was including the conclusion of Zero Hour in this as well.
Imagine how much more interesting it might have been if in Zero Hour the Shuttle Pod had been fired on by forces of the Imperial Kahnate and Archer had been found and dragged before a powerful but clearly ancient Kahn himself.
Doing that would have made the later augment storyline much more personal.
Instead we got nazis