When I started playing I saw that Resistance had more global control. I just checked, they still have (55% R to 45% E).
Anyway, in my case, the decision had several reasons. As far as the narrative goes I sided with Resistance, but thougth to myself: hell, it's time for a change. There was also a little bit of "transhumanists vs. bioconservatives" orangecat mentioned, and then maybe a little bit of: a) I got an invitation from a Resistance guy so I thougth going to the other team will be more fun, and b) I have small negative feelings toward Ada (because of the overblown popularity of A. Lovelace) and small positive feelings for Jarvis (AI from Iron Man movies!) :).
As somebody at my office put it: "Transhumanists versus bioconservatives...you have to ask?" But yeah, it would be nice to have some more resistance targets around.