Ok, here is my view on the issue.
"noble" brotherhood of steel: the brotherhood in fallout 2 gave me the impression of having transformed into something more noble than what we see in fallout 1 (or even the "western brotherhood" in fallout tactics). Nonetheless, the "outcasts vs Lyons" concept is a canon friendly explanation to what we see in fallout 3. I believe that Bethesda wanted to use the enclave and tried to avoid contradictions with fallout 2. The result is a not very "original" story, but it is canon friendly.
enclave: Eden's enclave doesn't contradict what we see in fallout 2. Again, i believe that Bethesda wanted to use the enclave and tried to avoid contradictions with fallout 2. The result is a not very "original" story, but it is canon friendly.
"fast" ghouls: strangely, i have not yet read any comment on this issue. In Fallout 1 & 2, ghouls were slow moving beings. In Fallout 2, the PC meets a ghoul doctor (in Gecko) who had actually seen the hero from fallout 1. The ghoul says that he noticed the hero, because he (or she) was running while ghouls could only walk. I guess that bethesda wanted fast-moving zombies, so they had to make this change. Personally, i would have chosen to make them slow and hard to kill, something similar to the "night of the living dead" concept (and at the same time more lore-friendly).
"daring dashwood": How could he have met Argoyle (his ghoul manservant) before the war, if the war took place 200 years ago? Ghouls can live that long, but humans can't. This is not a canon-thingy, but it is strange nonetheless.
super mutants: they really don't look like the talking heads form fallout 1 & 2 (don't get me started on the behemoths) but that is not necessarily a problem. They were created from a somewhat different strain of FEV... In the old days of this forum, when flame wars raged between "purists" and "beth-boys", a lot of people blamed bethesda for turning super-mutants into "ogres". I played Fallout 1, 2 and tactics, and 90% of the super mutants i found were hostile and not eager to talk. The only exceptions were:
fallout 1: Harry (i wouldn't call him smart, though...) and the lieutenant (my favourite fallout 1 NPC)
fallout 2: Marcus and the other super mutants inhabiting broken hills.
tactics: i remember a mutant scientist screaming something in the lines of "we are the only ones who can defeat the calculator, so we must find a way to reverse our sterility", then attacking me.
General Fallout feel: Fallout 3 is well made, but there is something missing... I advise all of you to download the "classic fallout music" mod from fallout nexus, which made me feel a sweet nostalgia.