I think one of the tricky bits of the Geneforge series is that all sides are equally obnoxious. I find myself wanting to do the opposite anyone tells me to do, no matter who they are. I'm not sure if this is just Jeff's writing style, or if it's something inherent to the nature of the world and story. Shapers have lots of power, and are bureaucratic and arrogant. Rebels have used a lot of the cannisters and are mutated and arrogant.
Just remember that you can replay the game as many times as you like. I played GF3 part way through, then started over again when my hint book showed up.
BTW, I recommend the hint book highly. You can read only the hints you want, or only look at the maps, or whatever. Also, it means more money to Jeff and company.