I don't think the problem is so much that the story "ended" the game.
Neither do I. The problem is that the game very abruptly presents you with a clear-cut, black-and-white choice of "Be a martyr or be a selfish asshole," completely ignores the fact that there are other options that ought to be available to you (stacking up on radiation resistance, for example, or sending an immune companion in), and then gives you an ending cutscene that consists of nothing more than condescendingly patting you on the head for being good or condescendingly frowning and shaking its head at you for being bad.
I think the Broken Steel ending was an improvement.
I agree, but only for the reasons I mentioned above.
This is a game, first and foremost. I prefer open-world games to be open-ended even after the main story is completed.
I strongly disagree, at least as far as Fallout is concerned. By having a concrete ending where the futures of the settlements and characters that you encounter are explained, it confers a powerful sense of responsibility on the player. Your actions have consequences, and if you care at all about the world you're exploring and impacting, you need to use your considerable power wisely to make sure that everyone gets the ending they deserve. In F1, F2, and NV, if a particular ending popped up that I hadn't planned for, say, as the result of a quest I forgot or didn't bother completing, it felt like a punch to the gut. It wasn't that the game itself was outright calling me an asshole, unlike F3 (seriously, that game was way too judgmental, especially with Three Dog pretty much chronicling your every move), it was that I felt responsible for neglecting something that needed my attention.
That all goes out the window if the game just keeps on going. It's back to the usual "just do whatever, whenever" that most open-world games already adhere to. I'm sure that some people prefer that to the distinct ending, but personally, I felt that it was unique and cool, and I'd hate to see the franchise drop it.
The problems is how Bethesda handled it. Your actions throughout the story don't really impact the Capital Wasteland, not because the game continues after the ending but because Bethesda simply didn't code it that way. If Fallout 3 was designed better it wouldn't be a problem. I feel like laziness on the developers part is to blame here. Oblivion made the same mistakes.
At least blowing up Megaton had a noticeable change on the game-world, although that wasn't handled very well either.
I'm not really sure what you're talking about here, or how it's any different to any of the other games in the franchise. The big changes happen
after the events of the game. Years and years after. They're long-term changes, not immediate ones.