ShadowWulfe: Five factions in 1?
I've helped the rebel humans, but I figure if I want to join the "bad guys" I can still kill them anyway.
Awakened feels like the "Canonical" (unless savegames carry over?) faction.
Obeyers seem... obnoxious.
Takers seem like the most entertaining group to join.
I think I'll go ahead and join Awakened for the first time.
I was just kind of wondering around WHEN to join a faction?
*spoilers for canon geneforge 1 ending below*
I wouldn't worry too much about getting the 'canon' ending to the geneforge series. Regardless if you are ro-rebel or pro-shaper, you will get endings that don't mesh with how your philosophy. two of the games have canon shaper endings, and two have canon rebel endings (with geneforge 5 having no canon ending, since it is the last game). It's a shame, because it means that you will inevitably reach a point in the series where you will be thinking "my character from geneforge x did *what?* I would never have done that". IMHO, it is best to just go with whatever faction feels most natural to you, because the sequels only follow one path, ignoring the dozens of alternate endings players may get.
Unaligned (loyalist shaper) is the canon ending for geneforge 1
As for joining a faction, I suggest just doing as many quests for them as possible, eventually they should let you join, if they don't offer membership outright. Joining factions has always been somewhat straightforward as far as I can remember in all of the Geneforge games except 3 (where there are only two factions anyways)