No, Marvel is utilizing characters under their control and are responsible for. It's the same faulty logic Saphiron employs in deciding that giving the Warden a voice is the same as giving Solid Snake a different voice actor. Players are far more likely to take issue with the game altering their PC. DA:I already does this: it decided for me that my Warden would abandon his wife and child to go off in search of a cure for the Calling.
The scenarios are not equivalent.
Witch Hunt was criticized to a large extent due to its under utilization of Morrigan, who appears in a brief cameo.
GoA, on the other hand, is a glorified side quest.
You mean the complaints of fetch quests being thrown at the game? That's not due to bugs. That's due to game design.
Resource management is an issue because the more world states you have to take into account, the more difficult it is to provide a satisfactory narrative while providing brand new content. This is made even worse in that developers will have to provide for an original protagonist in addition to the Warden. They're having enough issues as it is with the import system.
No, Marvel is hiring writers to do that for them. The writers all have their own vision for how the characters should be. Sometimes those visions conflict with what fans of those characters envision. And no doubt there is some CBG out there right now ranting in his blog about how Tony Stark would NEVER have said THAT because "reasons", and how OoC that was, and so on. You're right that fans don't have control over Marvel characters, but the point is that they still have certain expectations for those characters. If we all lived in fear that our expectations would not be met, then we would have no sequels.
Also, the Hero of Ferelden is not fully ours either. That character is mostly BioWare's. Even ignoring the EULA which has all of us consent to BioWare outright stealing our custom characters, you have to remember that each line of dialogue our CCs have are all written by BioWare. We expand our CCs through BioWare's writing staff. That said, no one in this thread is saying that BioWare should bring back the Hero just to send the character down a one-track, top-down, one size fits all type of storyline. BioWare should create multiple options for our CCs and let us choose the path that best fits.
Now, as for what your CC is doing in Inquisition; yeah, BioWare wrote another story. That's no different from how BioWare dictated that your CC left the Circle, or Orzammar, or the Alienage, or Highever. No different from how BioWare dictated that your CC became a Grey Warden (ignoring the "Skip the Joining" exploit). No different from how they dictated your CC had to unite Ferelden against Loghain and then the Blight. Face it. Your CC is forced to do things all the time. Where we the players come in, is regarding HOW our CCs tackle the problem and why.
For example, my primary character the Hero King of Ferelden, would obviously want to preserve his own life, and also help the Wardens who are still people in need regardless of the actions of a few of them. And of course he trusts his wife Anora to run things. And of course he trusts the Inquisition which has already helped Anora, Leliana, and Morrigan, not to mention Ferelden as a whole. So in this case the story fits my CC perfectly, and this is despite the fact that he dislikes the Grey Wardens and disapproves of what they do.
BUT! My secondary character, a bloodmage who did the Dark Ritual with Morrigan and went with her through the Eluvian, drank the Power of Blood concoction. He should be able to live for ages now, just like Avernus did. His longevity DEPENDS on the taint. So why leave Morrigan and Kieran to search for this? Well, that all depends on my character's motives and personality, which I get to define. In my case, my bloodmage is selfish and greedy, so while a cure would not benefit him directly, he could use the cure as a means to control Wardens to his ends. You saw what the Wardens did out of fear of the Calling. Imagine what they would do for a cure to the taint.
So it's all in how you explain this in your CC's own thoughts. And if there is no way to explain it, then ignore it. I mean, how many times during Inquisition was your Inquisitor faced with options that he or she would never pick if you had your way? You go with the one that best fits, and if that doesn't work, you ignore it and move on.
This would not be difficult. BioWare would create multiple "Origins" stories for our Heroes. And there would be a simple generic one for a new character similar to how it was in Awakening with an Orlesian Warden.