Well, it seems I was a bit late for that party yesterday. I'll drop a couple of thoughts anyway.
One thing that I didn't see mentioned, which I think is the key to understanding why people are upset about FO3, is that Fallout is by all means a piece of popular culture. A work (of art if you wish) intended for the public. It is also successful. Maybe it's not the most famous piece of digital entertainment ever, but still it constantly enjoys praise by most people interested in its genre and it always has a reservation in any "best RPGs" list. It has therefore attracted an audience that, as it happens in such situations, consider it as belonging to them, regardless who the legal owner of the ip is.
Now you may not agree, people often don't. There are two opinions about this sort of thing really, both very valid. Some people say that the creator or the current owner of a work is allowed to do whatever he wants with it without having to suffer any deprecation (or whatever it's called). But consider this: if you just happened to come into legal possession of a van Gogh painting (say for example that you inherited it) would you consider it your undeniable right to paint over it and alter it in a way that it would be more fitting for decoration of your living room? You would have every legal right to do so of course... but you can probably see that it just feels very very wrong. (The example is extremely exaggerated of course, since a Fallout sequel is by no means a van Gogh original but an exaggeration is necessary to understand the game's fans if you're not one of them.) So if altering a van Gogh painting seems wrong to you, there's one logical conclusion: you might be the legal owner of it
but it doesn't really belong to you. It belongs to everybody, it belongs to the public... it's not the painting that you own, it's rather the responsibility of preserving it and guarding it.
In extension, the creator himself is ultimately charged with the same responsibility regarding his very own work. Some people argue that once you 'release' your work to the public, it doesn't belong to you any more. The proof to that is that this work is from that point on open to criticism and interpretation. It's a pretty serious matter actually... for the creator to maintain such total ownership of his work, the only way is application of censorship which, most would agree, is not a good thing. Example: If I buy FO3 I consider it mine... why? because I can interpret it any way I want. I may want to do nothing more than spend all my gaming time sitting in a bench in Megaton watching at the sky, and I can claim that FO3 is, for me, a 'sky-watching simulation'. You would probably think that I was an idiot and you might say so, but the truth is, neither you nor Bethesda can forbid me to do it... well they could, if there was a law that would allow them to have me arrested if I didn't play FO3 the way it was intended to be played, as a 'post apocalyptic RPG' or whatever. But since there's no such law and we don't want such a law to ever exist, then I am virtually the absolute owner of my FO3 game - maybe I'm not the owner of the rights to sell my copy or to make a sequel or to change its code etc. but I'm the owner of my gaming experience no matter what, and that's what counts for me.
I personally like to draw a line at some point. In order to not go to the other extreme, I consider that someone has every right to create a work the way they want, as long as it satisfies all legal requirements. I am willing to overlook or accept any controversial features of it if, I believe they derive from honest creative vision. ie. I would praise FO3 unconditionally, if I believed that it is different from its predecessors because its creators honestly felt that this was the best way to provide a seamless, unique and beneficial (why not) experience, even if that experience was reserved for a selected few that would be able to 'get it'. Unfortunately I don't believe that. I believe that Bathesda are essentially 'crowd-pleasers' - people willing to compromise as much as possible in order to please as many people as possible - always within their abilities and skills of course, so don't argue that in such a case they could be making casual games for mobile phones, they probably could, but it's not what they know how to do best, such a thing may sound lucrative at first but it would involve great risk as it would take them way out of their 'comfort zone'.
As such I feel I have the right to feel in a way 'betrayed': they took something of 'mine' and they sold it to someone that didn't care about it in the first place.
If you think I went out of topic, well... I think you're wrong
But to make it clear here's my conclusion: My biggest issue(s) with Fallout3 is that it was too different from it's predecessors without taking any actual risks whatsoever.