Dragon Age Origins:
1) I wish there had been an option to confront Morrigan about what her real motivations were, and adopt a 'No more of this stepping around the issue - just tell me'. I feel like Alistair has a valid concern when he brings this up during the 'let's gossip about the party members' bit. She and Flemeth are obviously up to something, and not confronting either on the issue, is setting yourself up for a massive fall. Basically, it just makes you look like a total fool going along with it, because its Bioware exploiting the fact that nobody is really going to dismiss a party member over this, because they'd be risking content. But leaving her unchallenged and letting her stay, is such a massively foolish move that many player's character simply wouldn't do, if they were roleplaying them as they would in every other circumstance. But again, because its a party member, you feel obliged to go along with it.
2) I agree with Sten about the dubious action that the Dalish are taking (i.e they were going to run away and ignore their oath to help fight the darkspawn, and are only still there when you find them because they were attacked). Their solution is to send you on your own into a magical forest known for illusions that trap the unwary inside forever - without a guide. And this forest is teeming with (what are essentially) one hit kill enemies, and again will not send anyone to help you. Your party would have to be the stupiest people on the planet to agree to such terms, and you have to wonder at the trustworthiness of people who would make such an outrageous demand. So basically, I wanted the option to just tell them to screw off. I'm not saying the whole quest should be able to be voided, but I would like your character to be able to voice opposition to such ridiculously selfish and unreasonable terms, and maybe secure some help (i.e have a Dalish party member as a guest or full time party member).
3) I wanted to be able to drum up support from the Bannorn, and visit lands that were under Darkspawn attack. Think the opening section of Awakening, where the Vigil is under assault. You should have been able to do some of that, and get allies among the Banns. Having Redcliffe as your only allies, seems silly and Gallagher Wulff has a fair point when you meet him before the Landsmeet, as he asked if you're Grey Wardens and are supposed to be fighting Darkspawn, then where the hell were you when the south of Ferelden was being sacked? He doesn't expect you to destroy the whole horde yourself, but you could have helped evacuations, and done something at least.
4) An obvious one which has already been mentioned, but the resolution to the Landsmeet is very silly. The compromise that Riordan proposes is a fair one, and would satisfy the needs of justice. Its been established that regardless of Loghian's crimes, he was only doing it all for the good of the nation. That doesn't excuse his actions, and being made into a Warden is still a death sentence. Alistair's objections are understandable from an emotional standpoint, but clearly out of line. You, Anora and Eamon can have engaged in serious political wrangling to get a compromise that everyone can live with, you have just fought a battle of words in the Landsmeet to convince the Banns that the Wardens are not political opportunists, Orlesian puppers and tyrants in waiting. If Alistair's first action as King is to execute a man who has surrendered, how does that look?! Especially as he then goes on to seize lands and give them over to the administration of the Wardens, whose members typically frown on such things (Riordan expresses disdain for Wardens who do such things, and Duncan is clearly against such practices too). Nobody really wants to lose Alistair and the game doesn't really feel right if you lose him, but his stance here was so unreasonable. And the 'chop Loghain's head off in public, so his blood spalshes over his daughter's face' is so barbaric that it feels like you've stumbled into 'I, Claudius'.
Dragon Age 2:
5) The whole way that mage characters work in Dragon Age 2 should have been looked at. Considering Kirkwall is so anti-mage, its beyond silly that your Hawke and family members can stroll about in robes with huge staffs, slinging spells and with nobody batting an eyelash. You cast spells in the Gallows Courtyard as soon as you arrive - right in front of City Guardsmen, and they don't comment. You can cast spells in front of Cullen when you are aiding him against Willmod, and he somehow manages not to notice. Its extremely annoying, and undermines a core principle of the narrative.
But how does this fit into decision making? Well, I think that particularly a mage Hawke should have had access to (or even be forced to be) some kind of Spellsword/Arcane Warrior type. The game could have insisted that you adopt such a guise when around Templars etc, so as to arouse less suspicion, and let you be the more obviously 'Staff and Fireball' type when you are travelling normally. Basically, it would have been nice if the Mage Hawke could have been given a sort of 'Clark Kent' talent tree to disguise themselves. I just think that the game should have had some way to account for if and to what extent you were trying to be discreet around people who would have a problem with you being a mage, and factor that 'choice' into the narrative at various points. (I.e so if everyone knows you are a mage, then you have nobody to blame but yourself, because you've been fireballing your way around town, but potentially reward you for discretion by not having Bethany arrested or something like that).
6) Another obvious one, but the whole final Act of Dragon Age 2. I just feel that the final stage of Hawke's rise to power naturally should have led to becoming Viscount. You could get there by various means, but only allowing it to happen by siding with the Templars was a huge mistake. I don't really want to go over this again, as I've spoken a lot about it recently. Bascially the whole final Act is rushed and unfit for purpose. It would need a complete overhaul of all its missions, and its problems go beyond those that could be fixed with a simple 'If only you had this choice'.
And probably lots more, but they'll do for now.