The two largest story flaws lay in the poor sense of motivation and the sheer loss of an epic scale. To address the second, in most Fallout games you felt like you were a normal person thrown into this epic fight. Wether you chose the good or evil spectrum you felt big implications. Even though the combat may have been horrid running into battle with the BH:OS to liberate Project Purity from the Enclave felt, EPIC. Looking for the Purification chip from Fallout 1 was tense, as you knew you had little time to work with. New Vegas killed it. You never feel like anything you do has a large scale implication, and you certainly never feel heroic. It's always working as an agent, recruiting, preparing ect.
I honestly don't see how New Vegas is any different from previous Fallout games in this regard; the war between the NCR and Legion is no small fight, it's much bigger and much more important than the war between the Brotherhood and Enclave in Fallout 3. Not to mention I'd call impacting both the entirety of the NCR and Caesar's Legion in addition to the Mojave pretty "epic", but I don't know... maybe I'm just crazy like that.
As for never feeling heroic, well that depends on how you play the game doesn't it? I performed selfless "heroic" acts in New Vegas; maybe the main quest doesn't put you on a pedestal, but then again neither did the Fallout 1/2 main quests... you were just the poor sod unfortunate enough to have been chosen to find the water chip and stop the super mutants, and in the case of Fallout 2 find the GECK and stop the Enclave.
Even the boss fight can be so ridiculously dismissed with some barter skill, like one second it's this devoted tank of a guy fighting for what he believes then you pull a hat trick of snappy money related comments and he's suddenly like 'Oh yeah, I'll just turn invulnerable and cower in this tent while the war suddenly ends.' I mean honestly? Four sentences of common sense ends a long stretch of ruthless warfare? In what world!? That in itself ruined the whole feeling of a last resort war for me.
And how is this any different from how you can convince Autumn to stop fighting at the end of Fallout 3? At least Lanius is harder to convince than Autumn was.
And to wrap this section up, when you finish the game nearly no matter which way you go about doing it you feel like you were working for the wrong side. They either were asses to begin with or they went mad with power. Sweet.
That's the point, there is no right or wrong answer to what's best for the region.
The other major issue which I previously mentioned is kind of a tie in, but I will address it separately. In Fallout 3 you felt the urge to press on and look for your Dad, all the while you did any odd job you could for respect among the people and a bit of money for medicine. In new Vegas reputation makes committing crimes so easy and the lack of karma really affecting [censored] all I don't feel the need to do any side quests.
How does reputation make committing crimes "easier" exactly? Karma has never really impacted much of anything in the series, and it certainly never made committing crimes more "difficult"; especially not in Fallout 3 where you could change your karma on a whim by donating water to beggars.
Talk about not feeling motivated, the whole prologue with hunting Benny transitioned so abruptley into you fighting the people's war that it wasn't even laughable. You didn't feel like you belonged in this war, you just got plunked in via a recruitment mission, leaving really no reason to ambitiously chase after victory.
Would you have preferred the storyline stated that the Legion ran over your dog with a chariot? The game leaves your character's life open to interpretation so that you can fill in the blanks. You provide your own motivation for the Courier, and if you don't want to do that then I don't know what to tell you; just because the game doesn't spoon feed you a motivation doesn't mean one can't exist.
That's my two cents anyway. I can't say that I find the things you consider to be a disappointment problems; thus I voted "no".

I have to agree with the "lack of motivation" part, like Yahtzee said in his review (more or less) "People assumed i wanted to track down the guy who shot me in the head, but to me the fact that he shot me in the head was an excellent reason to not go after him!".
Except you kind of have to unless you want bounty hunters chasing after you for the rest of your life.
Fallout 3 had a more personal take on the story, which give better motivation.
Fallout 3 also had a more pre-defined protagonist, and a much more linear main quest which could and did clash with the player's vision of their character.