Actually Avellone just says Independent is his personal favorite (Which is what he likes not what the Courier would do. which is what your op for the characters were directed at.) I'm sure some devs of the original Fallout's favorite ending was join the master doesn't mean it happened. I'm asking what in-game thing really points to you to think the Courier would side with anyone but the NCR? The only other option I can see that would make a bit of sense would point to House. He's delivering the chip which is his job and that he's obligated to fufill it. Again though just an opinion in which I'm curious about yours not a devs . I try to interpret what I see as a book, and it's a bad idea to constantly hint at the failure of a nation and then say "LOL NVM they've got this" as the ending. The game is FULL of people saying the NCR is going to fail; same goes for the Legion. I WOULD agree with you if the Courier had plenty of dialog options to support the NCR. In this case, that would provide the game with an overall tone of "the NCR are the good guys, and if you don't do something to save the NCR, it'll die," but the Courier doesn't have many options to support the NCR vocally, if at all. The only conversation I can think of where the Courier voices an opinion about the NCR (save for convos with Ulysses, where he'll give similar praise to the Legion if you're a legion supporter) is with Captain Parker, and that was a negative comment the Courier voiced. Hell, in Lonesome Road, correct me if I'm wrong but if you want to be peaceful with Ulysses, you boxed into saying "You think I care if you bomb the NCR? Go ahead," even as an NCR supporter.
Short and sweet: I'd agree with you if the Courier had opinions every now and then that he could voice about supporting the NCR, but he doesn't. He can diss on them; he's more than capable of that, but he can't really support them through dialog.
So what remains? Who does the Courier support via dialog? Well, no one, to be honest. Ok then, we can't look to him for implications of what army the canon Courier supports. What about his surroundings; what about others? As I said, it's bad writing to say "this army is doomed LOL NVM." If you're gonna provide the game with an overtone of "this nation is doomed," you should stick to it. Is there an overtone of NCR failing? Definitely. Ulysses, a very important character, despises the NCR. Cass, an NCR citizen herself, will voice concerns that supporting the NCR, while nice, might not be what they need and might only speed up their damnation; she suggests you rethink supporting them. Arcade, who is arguably supposed to be the "smartest" person in the Mojave (perhaps aside from Mr. House, but the smartest person who isn't a part of one of the nations himself? probably), supports an Independent New Vegas. Independent Vegas is also the least criticized; once House dies, no one says "we're ****ed, (closest being the casino owners will ask what will become of the Strip), but rather people call him an a-hole and voice that they're glad he's dead. No one says "this is bad, anarchy will rule the streets," no one says "Noooooo our great leader," no one says "Time to leave Vegas then."
NO criticism for Indy Vegas voiced by the characters in game. This is unprecedented, as every other major faction has strong critics: Legion is evil, NCR is corrupt and House is a manipulative jerk. Independent Vegas? No one says jack against it.
And finally, the story of the Divide. The Courier basically could've built up a nation, but due to his neglect, it failed. To me, this goes great with the story of New Vegas. The Courier has the Platinum Chip; the Mojave is his to craft and shape. Will he fail a second time? Maybe, or maybe not, but it's time to at least recognize that the Mojave is HIS nation now. To me, it's more fitting for the Courier to take the steering wheel himself under Indy Vegas rather than to try and guide another nation on how to build HIS nation.
For those reasons, yeah, I definitely think Independent Vegas is canon. If it weren't Indy Vegas, would it be NCR? Actually no, imo. Then it'd be House. Another point of discussion is that Indy Vegas/House provides the devs with an interesting situation where they're free to kill off ALL three nations or spare every single one. If Indy Vegas is canon, NCR and Legion are both free to make a recovery of sorts where they continue to exist in California and Arizona (albeit with ongoing problems, probably). OR they could bomb both to hell and say Vegas fell apart without House, becoming the Courier's second Divide. House is similar; doesn't fit QUITE as well imo (it'd kinda write off the possibility of all three nations falling and House would have to succeed; it'd feel really weird if New Vegas failed because people just stopped coming and the super-genius House never saw this coming), but it would still serve that purpose.
And finally, if you want my opinion which ending is best? I used to think House. Lately? Lately I think Indy Vegas... Thing with House is, people always say "he's selfish, he only cares about Vegas and only saved Vegas from the Great War." I used to think no biggie, because how is he supposed to save everyone, he's not REQUIRED to save everyone and I believe the Core Region would be nicer if we had three different nations that left each other the hell alone and did their own thing, so I like his selfishness. Lately though, I've thought about what he stands for, and then I kinda understand the complaints about him being selfish. House stands for capitalism in my mind, and look at capitalism today. There's always one person (or rather ok, in our world just a select few; in a world of 6 billion people with only 1210 or so billionaires though, yeah I think you get my point with "one person") who ends up on top and in charge, and that person calls the shots. The way I see it, House only saving himself (and Vegas, though his motivation behind saving Vegas is questionable) during the Great War basically kind of stands for the fact that by the end of the day, he's the most important and he's the only one that'll be saved in a Second Great War. Perhaps a better way to explain it is, we all know that New Vegas is nothing but a way for House to fund his new visions and ideas, correct? He basically admits to feeding off of the NCR like a leech, but justifies his actions by saying "the end justifies the means" and talks about his goals. Well what if, before the Great War, House leeched money off of the common man? He had resorts and casinos before the Great War, we know this. And where did that money go? Into saving House, that's where. Basically, people are just tools for him. I've always known this but supported him anyways simply because in end effect, I found his ideas good, so I didn't think it mattered. Now though? Now I dunno.
I find it ironic that, if you kill House and say it's "strictly business," he's still thinks you're a piece of trash. In that sense, I think he's a hypocrite. That's the exact code he lived by, and that you killed him for business purposes? Well, that simply means someone beat him at his own game. In the same way Ulysses says Caesar shouldn't be mad at you if you kill him because "you've proven his own theory to him," I think the same can be said for House. Those are the rules he insisted on playing by and thus he should be ready to lose by those rules. Surely good men with good intentions have died under House (or will continue to, such as The King), so his claims of all the good he wanted to do being a reason not to kill him are irrelevant.
I think House can basically be summed up by Dr. Hildern and Arcade Gannon. Hildern will send dozens of soldiers to retrieve the data of Vault 22, not caring for their well-being but rather only about the data. Arcade will reprimand him and say it's horrible that someone would dismiss the little guy and get lost within the big picture, to which you can either compliment Arcade on or say "but in the end, isn't it all just numbers anyways?" To me, this is the classic Indy vs. House issue. I'm somewhere in-between; idealist enough to agree with Arcade but realist enough to see House's way. However, what I've recently asked myself is if I could sleep at night if I were the one that supported this "big picture" thinking and made sure it became the standard, and to that? I'm not sure if I could...
Not to say I'm no longer a House supporter myself, I'm just....not sure now.