I've read conflicting reports, that they do change the ending and that they do not change the ending.

I've started out by playing a Rebel, so I have been using canisters.
My next playthrough, I will probably play as Shaper.

The nature of the story tends to make me believe that the effect should be negligible (we're already off the deep end), but really I am just not sure.

Also, I rather enjoy the inner conflict / adaptations of the Shaper politicians.

Id like to help ya but Ive been having some trouble myself with Geneforge 3. I still can't seem to find a non-violent way around the warped creator in the beginning. I really just don't remember how I got past it with my agent.

Did you check the MattP guide? I find that that is helpful if I'm confused (though the recipe lists are really the most helpful part... why are recipes not added to the journal when you read them?).

I ended up joining Trakovites for my first playthrough... damn they crazy. O_O

I played through on a no-cannister run, I didn't see it impact the game in any meaningful way, althoguh I have heard that the guardian at Kratoa-Kel will have slightly different dialogue the first time you meet him, I personally don't remember anything different from the time I met him on my cannister-crazy playthrough, both times he hated me for being a mutant freak. There is no reason to avoid cannsiters in this game unfortunately, one of the things that I did not like about this game, and IMO a huge step backwards from G4.

I remember getting that little leadership check at the bridge as well (the one where the unbound shows up right afterwards, I think?) on my no-cannister run, so I don't think that even that counts.

I disagree about the goal being to take the focus away from the player character, due to the amnesia plot, and the player's relationship with rawal. These serve to make the story very personal, and IMO the fact that neither of these storylines has any real payoff are real failings of the game. Going through the first time I was excited to see what effect my choice of class (rebel/shaper) or reputation (rebel/shaper) had on what my character wa before they had their little brush with insanity and amnesia. I was disappointed to see that not only did my choice of an shaper class versus a rebel class have absolutely zero effect on anything, but that the characters identity and the circumstances which led to their current situation are never expanded on. Likewise I wasn't thrilled to have the rawal control tool have as little effect as it did. I was afraid of overstepping my bounds and him finding out about it, leading totorture/death on my first playthrough, but disobeying him has effectively zero reprucussions. There are a lot of parts of the game which could have been good, but the fact that they are never expanded upon severely weaken the plot of the game, IMO.

And I finally finished a Shaper playthrough, with Taygen and Alwan.

A lot of things do seem a bit underdeveloped. I avoided killing Platano when I joined up with Taygen, and found out that it had no influence either way.
The plot could have been great with a more introspective look, but I suppose we got what we got.

If I was not so exhausted I would have more to say. The series has been quite a pleasant surprise.

I was considering emailing Spiderweb to see if their 50% off sale will ever include GOG keys...

Im glad you enjoyed Geneforge series. Im currently on the 3rd island in gene forge 3. Its a lot of fun once you use the gamefaqs faqs religiously :)

I haven't had any real problems with stats anymore and am enjoying the difficulty.

Shadowwulfe, I say this with the most sincerity, if you liked the gene forge saga, you've got to try Avernum's 2nd trilogy. It uses the same stat/skill system as gene forge, it has stunning like gene forge saga and unlike avernum 1st trilogy. They also let you make a whole party of up to 4 characters.

I emailed Spiderweb support to ask if the 50% off thing would give out GOG keys if/when it eventually comes here and he/they(?) said no (unsurprisingly, but it was worth a shot).

My big question is if I should wait or if I should just get it, and to me, it kind of depends on the length of time between the series coming here.

I haven't read a single bad thing about the series (from serious people).

I feel like the real meat of Geneforge 3 starts at the third island. The second island's monster generator part was kind of obnoxious. I only used Gamefaqs to make sure I didn't miss anything. I barely have time to play games so doing a different run through is a huge time commitment.