I guess I'll put in my two cents:
As of now I've gotten to Dhonal's keep, and I am quite impressed. Geneforge 3 is the most developed of the three games. Each one has its own unique attributes.
GF1 was interesting because it was the first. you actually got to make these creations and order them around. You got to learn about the shapers for the first time, and he history of sucia Island was very well written. The factions were not entirely critical to how you played the game, as they basically gave you free stuff and advice with what to do with the geneforge. Ultimately, the decision came at the end of the game, and for the most part, the endings were happy ones.
In GF1, you mainly got the perspective of the shapers from serviles who had gotten smart, had looked at the shpaer/servile relationship themselves, and decided whether they liked it or not. Also, later in the game, you get the perspective of outsiders who were new to the technology.
However, GF1 was still a little...primitive. The spells were few, the world really didn't change based on your actions, and the options for stealth/diplomacy were not as strong as the force method.
GF2 was also a great game because of the new creations and spells. There was a clever link between GF1 and 2, and world actually changed based on your canister use and what you say.
What I didn't like with GF2 was the factions. They seemed formulaic to me, and you really didn't get much explanation beyond "This is what our faction believes, now join us" from the faction leaders. In GF1, you got to hear from all three factions when you were about 1/4 through the game, in GF2, It takes you about 3/4 of the game to get to the takers. The idea that all four of them are at perfect stalemate isn't very plausible, and the missions they give you are redundant.
In GF3, you get an excellent view of the shaper world: Through the eyes of many different well developed secondary characters. The world is very fluid, as how you act in one island affects the other. Alwan and Greta offer great insight. You are given several choices whether to help the shapers or rebels or stay neutral, which don't automatically disqualify you from parts of the rest of the game.
Although only two choices does seem a little limited (keep in mind I've just gotten to Dhonal's keep).
They underground levels are a clever touch, and the stealth/diplomacy tricks are very well thought out. Rushing in full throttle no longer works anymore (at least not when fighting the four spawners/two servant minds on harmony)
That's my thoughts. Hope you enjoy the game as much as I am