Haven't read through the pages of reviews, but my impression was the same as the OP overall. I fully expect that there is a TON of film left on the cutting room floor. Something that felt completely out of place was the spontaneous trip to some cave by Thor that seemed solely to function for the purpose of a larger arc of exposition.
The short run on this movie was this for me: it was a severe mash-up of the various iterations of the frankenstein story. While not a bad idea in premise, the execution left too little room to flesh out the motivations of all the characters. While the paper media is not bound by the general constraints of time of budget, the modern movie if very much constrained by this as going over the 3 hour mark is not only difficult for the intended audience with respect to captive audience mode, but is also less conducive to a movie's answer to keeping the turnstiles churning to get more people in the seats during a day. That said, off the top of my head, here is the quick list of this movie's frankenstein story iterations:
1) Hydra as Victor Frankenstein - beginning with their exploitation of the twins, they represent the prototypical mad scientist hubris lacking in motivation outside of sheer lust for power. Hydra serves as the stand-in for necessary bad guy in this movie. They simply provide the starting catalyst for the series of events to follow.
3) The twins as the monster - In large part, these characters were not given a serious chance to allow their stories to emerge organically. Rather, they were given an origin through exposition with their initial conversation with Ultron. With their current abhorrations giving life by Hydra, they started out as minion monsters, lost their way with revenge still driving their motivations, and found new direction for their vengence with a sympathetic manipulative Ultron posing as a fellow monster that was made. Their turns throughout this story exhitibited many iterations of the misunderstood monster to ultimately find their own way as their perception of the world was opened from the one controlled by their creator(s).
2) Stark as Victor Frankenstein - While maintaining the glaring hubris that has been the mainstay of the Stark legacy to accompany the quiptical witticisms, Stark's motivations are made more palatable. Of the characters in play for this film, he has been closest to seeing the horrors that are knocking on our home's door. It is his xenophobia that drives him to the drastic ends for which he is justifying his means.
3) Bruce Banner as Victor Frankenstein and the monster - Definitely among the more interesting of these iterations, Bruce was served best in this film as the range demanded for this role was large if it was to be pulled off. Bruce is a monster of his own making. His story is well-known to the American audience. As a result, when he is pulled into the role of Victor Frankenstein again with the only compatriot in this movie arc, it is not surprising that he assumes the role of extremely guarded caution. Ultimately, it is curiosity, reason, and budding tenuous/conflicting trust/affection with both Stark and his other teammates that drives him to assist Stark and his initiative to proactively protect their home. This part of Bruce's story was most underserved, but Ruffalo and Downey were able to do enough to get this point across with the barest amount of on-screen time. It was the final bit of screentime for his character that brought the hammer of the frankenstein's monster allegory home for the entire film.
4) Ultron as Victor Frankenstein and the monster - Born as the monster and instantly flipping his role as the mad scientist, Ultron is an interesting character who's evolution of motivation felt rushed on screen. In undoubtedly trying to pin Ultron as the overarching frankenstein metaphor for this story, the themes were very overt to the point of bludgeoning. Even striving to re-invent his form to the ultimate evolution, he referred to this chrysalis was even referred to as "cradle" while this new form was waiting to be born. Spader did as much as could be done with the character of Ultron... and it was better than serviceable. Ultron was meant to be a villian but one that was very much an enigma that was continually showing us subtley different sides to itself. It was enough to make us ponder Ultron's ability to doubt himself at his core (curious personality quirk for a robot).
5) Which leads us to Vision as the monster - For all of the intentions that were poured into his creation, the consequence of his being was fully unintended by all parties involved. While the potential for this character is loaded to the hilt, his part in this film was not only rushed but given little more than characature treatment and eye candy for screen time. We may revisit this birth as a part of a larger whole as this series continues to play out, but for now he was every bit the placeholder in this film as was Hawkeye for the previous installment.
6) Captain America and Black Widow as orphaned monsters - While Cap had a bit more of his story re-hashed and solidified for what will undoubtedly be more integral for future chapters in the larger arc, his part was more of an anchor that took a back seat to Fury and Hawkeye in this film. His monster angle was more prevalent when he was staring down his creator's son and seeing that same hubris and sprinkled with that same wit. Black Widow, on the other hand, had a more insidious and revelaing side shown to shadow/mirror Banner's story to give this film it's most compelling screen time and heart as their stories were allowed to onfold in front of us. In many ways, their story was allowed to organically grow on screen the way that the twins' story was not.
In all, it was a summer blockbuster that didn't disappoint. There was plenty of spectacle to be had, and plenty for the fanboys to secretly adore on screen while hate on their message boards for deviating from their coveted canon. The story, at its core, is strong enough to hold its own with just enough heart to clear the bar for most critics to appreciate. Sadly, it could have been more with less, but the mandates of time and money likely would not allow for it to be what it was desperately striving to be.
It was a worthy entry, but it falls short of the lofty expectations that have been built by the empire that is now driving this gargantuan ship.