I think the issue is that the two main villains from the Netflix show were handled as characters themselves that were also part of the heroes story's, and thus given time for characterization that was more than just surface detail or letting just a costume or concept do all the work. In the MCU films, especially in terms of first outings (i.e. Super Hero Origin stories) the heavy lifting is being done by the heroes. Marvel is looking to establish these heroic characters as long term franchises. Iron Man 1 is Tony Stark's story, period. Steve Rogers is much more a presence in CA:TFA than the Skull. Loki, as seems to be the case with lots of opinions, is a bit of an outlier. His character was given a compelling backstory that was tied into THOR1's plot and the actor that they cast has knocked it out of the park every time so far.
The other villains have, even their defenders have to admit, been less than stellar in the writing and performing area as compared to Loki, Killgrave and Fisk. Skull,Ronan, Whiplash, Maliketh, Pierce, Ultron, Mandarin (whichever one in IM3 you pick)... They've either been overwritten (again... IM3, where, whatever one thinks of the "twist" it's clear from the arguments that defenders get into that what others see as director's intent just went over a lot of the audience's heads and landed behind them in a big fat "Meh", BO numbers notwithstanding) or underwritten. Ultron while entertaining, feels like a rushed antogonist to me. Ronan was a cipher of a villain. We are told EVERYTHING about him through exposition after all.
On the Netflix shows the villains got scads of development time, or at least we got to know them, their methods and quirks and general personality, quite well. The characters gave off a lived in vibe as opposed to just being a cog in the comic book movie machine... Which isn't all that bad actually. Not every villain has to be freaking Salieri or something. Not every CBM villain NEEDS to be Heath Ledger's Joker or as engaging as Hiddleston's Loki. Still, in comparison, too many MCU film villains feel "thin" in their characterization and villainy, though even then, you can have a not so complicated villain's back story that is straightforward but if it feels like the actor and the writing have made the character come to life even then it's not so bad. I think Roth's Abomination was by no means complex, but I think the evolution of the character, his simple motivation ect. were done well and paid off well in the movie.
I think what some fans, myself included among them, wishes that the MCU film villains were just a bit more fleshed out and given a tad more menace and focus in the stories, something that the two Netflix shows did very well.