Mmm. I have to agree.
Daleks in Manhattan wasn't great. Which is a shame, because I suspect that if you removed the Daleks altogether and replaced them with a new monster, it might stand up a little better.
What I'd like to know is where are these 'Art Deco Daleks' that have been mentioned around the Web? One thing I read about them was that they were silver and blue, like the very first Daleks in the classic series.
Incidentally, I think Dalek Sec's idea of creating a half-human half-Dalek hybrid may have been purely coincidental. We don't really know when the Cult created the Voidship and escaped the Time War (indeed, if they ever took part) with the Genesis Ark.
In fact, I'm surprised that the Cult didn't just exterminate the hybrid Sec more or less straight after he emerged.

"Crossing into established events is strictly forbidden. Except for cheap tricks."
- The Tenth Doctor, Smith and Jones