This list is opinionated but based on facts. The goal isn't to make fun of the games but to contemplate about what could've been and what could be.
Also, the flaws in question aren't actual character flaws (those are good!), but rather lackluster design or writing. I've covered the first three games so far and will move on to the last two soon. Fittingly, G4 and G5 have far less wasted characters.
Takers as a whole seem overly nasty. While an open choice is one of the game's themes, there is far, far more reason to join the other two factions, power aside. One of the reasons takers appear too evil is because there isn't much indication of shaper cruelty in the game, unlike the sequels. Needs to be more clear signs of servile abuse earlier. Experiments on serviles come to mind. Give takers a proper reason to be super rebellious. Make there be legends of evil shapers of the past. Have the player fight resentful Shaper ghosts. Heck, have the player remember shaper atrocities that they've seen. Have them find logs of how bad the takers had it. There needs to be more than just rebelling for the heck of it. Edit: Randomizer speaks truth as he mentions abandoned, toxic research labs. There should be more effect from this other than a few mentions. Remember G2 and that servile sickness?
Zachary has high potential. His demands aren't warlike, but sly and cunning. He could've been a mastermind who'd use you as a secret agent for his redemption. He could've tried to fully recover from the damage done. Lastly, he could've had secret influence in the land. Instead, he has almost no power, locks you out of much of the game if you side with him, and gives you no help at all. A waste of a good character. I see Zachary as a foil to Barzahl, a person who excels at being a leader and strategizing. Joining Zachary shouldn't mess with the rest of the game; it should be a secret oath. Imagine if he told you something along the lines of "Do what you must, say what you must, in the end only the results matter.". Imagine if there were spies in every settlement, each with their own plans on how to restore the old laws. Imagine trying to capture Barzahl alive, perhaps? Zachary would probably want that. Maybe he'd blame everything on Barzahl, the double-traitor. Zachary is obviously flawed and a bit greedy, but there's better ways to point that out - being slimy doesn't mean he should be weak.
As for Barzahl himself, he fits his role very well but shows little character outside of it, by making him clearly inhuman, he loses his character. Later in the saga, the potential of mastering canisters and reshaping properly is put in the air. Instead of blindly embracing power, Barzahl would surely be a better character if he sought to fully master and control it. He'd still be incredibly illegal and opposing to other factions, but instead of a power-drunk fool he'd be perfectly sane but obsessed with mastering old secrets, which would also make joining him seem less intimidating while still being anti-shaper. Picture him as someone who's clearly indulged in the forbidden ways but is on the brink of finding out how to counteract the negative effects - he struggles with self-control but is ultimately a pleasant person with grandiose plans. He's seeking progress, not power. Now that's a much better character.
Litalia is more an antagonist than a rebel. All she does is make a mess everywhere she goes. Helping her is more evil than anything. Whether or not you side with Litalia should give you an evil/good ending, not a shaper/rebel ending. There should be ways to help the rebels without being a horrible, horrible person. Being horrible to shapers is one thing but the actions done in G3 are misguided and foolish. You should also have an option to be a full rebel but still kill Litalia for her actions at the end of the game.
Lack of true rebels on Greenwood. The island of literally no choices. There's a group of rebellious people in a place near Kentia...they don't do anything. Swap these guys for a proper rebel group. Greenwood doesn't have much shaper monitoring, it's a perfect place for all sorts of illegal research or even a black market. Have a quest to convince the Kentia leader to allow the rebels to do their thing safely. A little shady business hurts no one, and the Kentia leader isn't a shaper. It's good potential for this sort of thing. Fixing the rogue problem should make you quite convincing in this regard. You leave the island either way but you can make choices at least, this way.
Lankan is a [censored]. A good leader sure, but a total fool with a horrible goal as well. Remove that canister gubbins. Lankan's goal should be to win against Diwaniya and fight for the rights of his people. What if you killed those spawners but told Diwaniya that Lankan and his men helped solve the problems? What if you worked to actually make him more powerful, instead of just bringing him a canister? Steal research, get rebellious people to defect, get supplies and so on, until the settlement is actually a threat to San Ru. Make negotiations and get Diwaniya to break his word and treat Lankan as an equal. This guy's backstory is great, but then you meet him and it all goes downhill.
Diwaniya is okay but isn't anti-rebel. He's anti-rogue. Fixing the rogue problem should get you off the island but shouldn't actually solve the island's problems. If being pro-rebel means you get Diwaniya to acknowledge Lankan, being pro-shaper should be about getting Lankan to bow down and face justice. Convincing people to desert him seems like a textbook way to crush the rebellion in Harmony Isle. Do a series of quests that improve the state of San Ru enough to get everyone but Lankan to leave, and then maybe he'll run off the island or get jailed in defeat.
No rebels on Dhonal's Isle either, really... I think a rebel outpost near the Creator dungeon would be a fine addition. A secret place that you'd know where to find if you were pro-rebel, or that you'd massacre with the army if you were pro shaper. I feel that people in this outpost would be all about secrecy, gathering as many people as possible and amassing a force that will eventually get Rahul to surrender. Guerrilla attacks and the like. The creator and rogues are a distraction, these guys should be the solution (for rebels). Dhonal's Isle is one of the few locations where there's a very good reason to directly attack the shapers. It's important for the rebels to want to specifically slay the shaper authorities though, not just everyone. Loads of assassinations and sabotages, maybe with a bonus quest to kill Rahul later once you're powerful enough.
Rahul has no character. His actions are fine but he's a shell of a man. Give him backstory, give him his own views that aren't just generic propaganda, give him a proper goal. Rahul needs to be against rebels, not just against rogues like Diwaniya. A history of dealing with rebel atrocities should be good. Rahul, survivor of five assassinations, quencher of six uprisings, and so on. Have Rahul lead the charge instead of barking orders to Greiner. After killing the rogues, Rahul should be the one to find the rebel outpost and start the raid on it. It's a moment that shows both shaper cruelty and shaper justice at the same time. Think of him spouting mad revenge for what the rebels did to the isle as he goes on a killing spree, shocking even his own men. For a pro-shaper, that's a display of loyalty and care about his people. For someone less-so inclined, that's a cue to reconsider what they've been doing...
Akhari Blaze needs to be more than a villain. Either this or there should be another leader figure for the rebellion that's less hateful and more geared towards having peace, but without old shaper laws.
G4 and G5 coming up later as I still have some analyzing and brainstorming to do.
What characters would you change if the Geneforge series gets remade?