Just a couple of adjustments and you open up a new world of story telling.
1) You're not of humble origins, just unknown. You hail from a different land, a secret order, or have some unheard of gift. You're already a hero but don't deserve it. You're already a hero but this new threat can not be handled by the abilities you currently have.
DA has origins that allow you to start as a nobody or a somebody. I am under the impression Hawke from DA 2 is starting as a hero that may or may not deserve the title
2) You start with either one or no companion. This companion might be completely useless but valuable to you and still requires your protection. (i.e. little sister, etc...) Companions only join you in exchange for favors, and not usually willingly.
Again, this is already found in bioware games. DA and ME2 have companions that are not willingly or at least begrudgingly joining your cause which is why they can become disloyal at certain points. Not all companions are heroes doing it for the good for all kind.
3) You're not recruited in to an elite organization. You're already a member, the founder, are exiled from one as part of the story, or are never part of one. Maybe you choose which of these you go with. Maybe there is no elite organization, you're trying to found it in response to a threat.
Again, DA origins allows you to start as a member of some important organizations or you can be of nothing. Of coure, they're getting rid of the origins so I might see where you could take issues with this one. I hoped they would expand on them myself, sounds like they are just throwing them away.
4) You experience no tragedy at the beginning. Instead, you expereince tragedy in the second act when the stakes are much higher. Or it turns out your actions are a tragedy unfolding. You may or may not know this. You may or may not have a choice about it. (Oracle at Delphi?)
Tragedy tends to get people to act who would not act before. It's just a part of human nature. Having said that, I don't necessarily see a problem with this suggestion except that it's not really changing anything so much as shifting it around.
5) You're presented with 7 optional hubs from the start. Only 2 can be completed, with the rest being considered failures and hurting your relationships, or limiting them, appropriately. You choose what's important and what you have to give up. (Optionally you can play your strengths against your enemy's weaknesses and keep up to 4 open. You're not told this, you must discover it.)
This can certainly be done, but I think a lot of people would throw this in the not fun category. This is still a game. You're talking about a no win situation here. There are some of those in DA and ME2. You need to get past discovery ideas though, the internet pretty much destroys surprises. Hell you don't even have to be looking at a guide, just coming to this forum and reading comments reveals a lot of spoliers. Again, not an impossible idea, but one I wouldn't like.
6) The enemy has trouble tracking your movement at first. They can't begin to thwart you until you finish at least 1 hub. Further, they try to recruit you, and can do so sucessfully. Sometimes their inteference backfires, instead providing you with an advantage.
I see a potential problem with this idea. Your essentially calling for two games to be wrapped into one. I don't know if i would choose a 10 hour game over a 20-30 hour game because you can join the bad guys. I don't find much appeal in joining bad guys kind of scenarios, so I wouldn't play it a second time through. Essentially, you cut the game in half for a person like me which would definitely me in the not good category. As for tracking you down, some of the games its not even apparent who the real enemy is so they having them track you means little. I assume by tracking you mean they show up and you fight them of course.
7) There are 3 different enemies in the game, and they're not working together. You can side with one or more of them. Depending on whom you work against they even help you at times. There are also 2 different "Good" organizations. Alliances can work in many of the tangles this web offers. Optionally sides taken and alliances formed and broken affect the hub selection.
This could be an interesting idea, but a complex one. We're dealing with companies who want to give less game for more money. It seems highly unlikely they'd offer this kind of complexity without stripping the game down to the barebones. I am not saying I oppose the idea, just very skeptical it could ever happen.
8) Morality is not decided in simple decisions, only in decisions of great personal sacrifice vs great personal gain at the sacrifice of others. Otherwise it only affects your relationships with others involved.
I am not a big fan of morality points or systems at all actually. I'd get rid of them if i could, or at least provide enough flexibility that you don't have to be good or bad ALL the time in order to have enough points towards the end. I think the system you are suggesting almost reflects DA's system where you don't take someone with you, they don't really react to your actions. I do think it might be nice if all the companions showed up for the really big decisions. I mean really, what the hell are they doing while you are knee deep in tunnels fighting darkspawn anyway?
9) Lowering your "Favor" with a companion is not always bad. Sometimes you need a hard boiled egg who doesn't like you all that much but is still on your side. Quoting Alpha Protocol "If they like you too much their emotions might get in the way of their decisions."
10) Your companions do not wait for you to act. Sometimes you need to catch up to them, sometimes you need to rescue them, and sometimes they leave and find you when you need them most.
I already mentioned I haven't been a fan of the morality, favor, paragon, whatever the hell Bioware wants to call it at any given time system. I hate focusing on points. For a company who claims to be all about story, they sure spend a lot of time trying to get you to base your story on their point system. Between the two, DA's was better than ME 2 for me.
Any one of those changes the formula. More than one and you start to get something really new and fresh. The numbers can be tweaked as well. Some of these I've not even seen before and some I've seen elsewhere, either done well or could have been done better.
For me, you present interesting ideas, but I am not sure many of them would actually create the kind of changes you are looking for so much as shuffle things around. 7 certainly has a possibility. You have to keep in mind, Bioware is also trying to do this story driven thing which, so far, works for them which means, like a movie, they're looking at pacing. They want to get you involved and interested right away and plan for climaxes and things like that. Shuffling things around might work in theory, but there is a lot of drive in that basic questions "who the hell is responsible for this mess" that can keep some going.
Autarkhos
Fantasy GTA, I can think of fewer games I would want to play less than what that name implies. I don't like the GTA series, haven't since the first one actually. I would suggest you take your suggestion to them, Rockstar, and not Bioware. They managed to put out a western after all that is getting good reviews, and not just from GTA fans.