You're ignoring the well known fact that Genesects aren't flippin' robots. They are cybrogs. There is a huge difference.
I'm not ignoring that at all. I'm just saying they don't seem emotive enough to be the main villains. Look at Articuno, Zapdos, and Moltres in the second movie. Same thing. They were very important figures to the story and were clearly sentient being, but they weren't "main" anythings and had only fleeting hints of actual personality.
EDIT: Damn, my example got Ninja'd. =)
--- My NIDOKING brings all the boys to the yard: http://goo.gl/ExAoe