Its not about scheduling an actor to appear on the show. The logistics problem is making the scripts mesh, when the way scripts are plotted is radically different for movies and TV. Admittedly, this is mainly a problem for having stuff go from TV to movie ( any upcoming movie will have its plot locked down upward of a full season before release, so any TV references have to be either edited in last minute, or from older seasons ).
Anyway, I think the biggest mistakes they made:
0. Green lighting the show in the first place, doing all the prepwork and initial scripts and such, and then "SHIELD goes kaboom!" The showrunners only found out after they'd done a great deal of initial work, and that undermined everything and forced them to go a specific direction with specific results.
1. Having Coulson's operation become the heirs to SHIELD, trying to operate like they can rebuild SHIELD and eventually have things back to normal. Given that the movies were not going to reintroduce SHIELD, it results in a narrative direction that just doesn't work. Either failure is inevitable, or else he has to succeed at putting together an organization that looks an awful lot more like SHIELD's mistakes than successes.
2. Going too big. The inevitable question with any big superhero plot is "Why didn't _____ help?" The MCU is big enough and broad enough that you can avoid this without too much trouble, IMO. AoS decided to instead see how hard they could smash on suspension of disbelief with a hammer, courtesy of the extended Inhumans plotline. You shouldn't write stories where there is literally no good reason to not get on a phone and go "Hey, Avengers? There's a literal world-threatening bad thing happening at these coordinates."
3. Too much HYDRA. Not only did it get repetitive, but it stripped the grandeur from them as a villain group. If they were going to use Hydra remnants in season 2, fine, that makes sense. There should have been *zero* Hydra in season 3.
Yeah, you can't go from TV to movie easily, and you shouldn't. The TV show is to promote the films, it's like the Star Wars Expanded Universe, in a way (and perhaps will also be WordofGodded away?). I think it's doable on a small scale, for instance, with a high amount of coordination, the Agents of SHIELD characters could have been running the bridge during the Age of Ultron final battle. The filmmakers would have known about the show and the potential crossover far ahead of time, could have had an episode where Fury comes and recruits them to get the Helicarrier out of mothballs, and another which covers the Ultron battle from a rescue operation standpoint. Could've been awesome. Now, in reality, that scene would have been shot during the actors' season break between 1 and 2, but it could have been a really gorgeous payoff, on the level with the Winter Soldier crossover. Who knows, in a perfect world, if the show was doing it's Season 1 numbers, they could have even gotten a super powered person into the Civil War with the same kind of shooting schedule.
But yeah
0 - See, I thought TV was flexible. They couldn't have twisted the AoS setup and initial cast to actually fit with the films, and like you said, adjusted the premise going forward to work. I think they had the same experience a lot of Marvel directors have and instead of having to bend hard or walk away, they were able to separate themselves from the movies a bit, which hasn't worked out well in the long run.
1 - I think the biggest sacrifice that they would have had to make, if they stayed coordinated, is changing the name second season, or late in the first season. The show wrestled with the "Agents of Nothing" on screen and they decided, as Coulson did in-universe, to stick to their guns. That sacrifice would have really shown that the show was part of the MCU in a very serious way. And I don't think the show would have lost much since all Season 1 collections would bear the new name.
2 - Agreed. It seems like spy thrillers work when there's a thing, a Pandora's Box, that they're trying to stop from opening. A sale, a virus being spread, an assassination. In superhero films, they open the box in the third act and the hero has to beat up whatever comes out and close it again. But AoS kept opening the box, whether it was Hive or Inhumans or cyborg thingies (though Coulson did close that in a funny way). A side effect of going to big: saying Coulson is an Avenger.
3 - Yeah, they kinda AIMed HYDRA, which is unfortunate.
Now keep in mind, there are a number of pressures in a TV schedule and breaking a TV show and spreading it around the writer's room, but here are my major problems with the conception of the show:
A: Not making it about a superhero from the beginning. This is a show set in the MCU, they should have intergrated a long-form superhero origin story into season 1 because 1) They Can 2) People Like It 3) People Expected It 4) It doesn't get in the way of a SHIELD storyline. At the time I strongly suggested Carol Danvers, and though I'm glad they went with giving her a movie, there are a number of other great candidates, including Quake, if they'd gone with that angle from the beginning.
B: Following the fandom, instead of the formula that creates the fandom. Everyone loves (loved?) Coulson, and for good cause. But the reason he was loved by everyone was the way he fit into the MCU. The reason they got into the MCU was because of it's slick streamlining and updating of tried and true concepts from Marvel Comics. AoS thought it could get the fandom without streamlining and updating tried and true concepts from Marvel comics and, well... not so much. AoS would have had a stronger following, with the exact same quality if the characters had names like Clay Quartermain, Elise Carson, GW Bridge and Jimmy Woo. To say nothing of if they'd actually taken on the SHIELD mythos. Imagine a Contessa Fontaine in place of one of the 5 generic HYDRA sub-heads they've had.
C: They dropped what made the short work. I think a similar thing happened with Agent Carter, where it suddenly became about somene who wasn't kicking butt and who wasn't dealing with Classical Marvel villains and super-science. They stretched the premise instead of expanding it. Item 47 was light, comical, badass and connected directly to a natural and necessary plot thread from the most recent Marvel film. Of course there are alien artifacts all over the black market! How could there not be? The quirkiness, what I think the show tried to keep, worked because those actors were funnier than they were attractive, imho, and because they had an excellent foil in Sitwell, who showed he was a worthy successor to Coulson, again, imho. For the show, they removed the foil, upped the attractiveness and youth, took down the comedy to a more rote scripted level and dropped the connection pretty quickly.
D: Centering around Coulson. This really is all of the above, but to bring this guy in, in Episode 1, with no explanation, and leave it as a mystery how he got back really misses the point of: his death is a huge deal in the movies. It send a clear message to me: "This is a show for the people who don't care about his death, because neither it, nor his resurrection are important." And if I thought the circumstances or results of his resurrection were going to be consequential, the show certainly corrected me. But what added insult to injury is that they discovered, I believe, that Coulson, as he appears in the MCU films, is designed to *not* be a lead character. He is the guy who always keeps his cool, even when interrogating someone whose decimated his men, he's only scarcely more than irritated. The world is blowing up around him, or a guy has him dead to rights at the convenience store, Coulson is cool.
That's the joke. So when the show puts him the lead, it needs him to be more aggressive to push the story, and so he becomes a lot more like Mal Reynolds, where he's this tortured man of deep conviction who puts on a happy face as a tactic, and in that he becomes, to me, more juvenille, and markedly different from the Coulson that I actually liked. And what's worse... if they hadn't needed to center it on Coulson, they could have brought Coulson back and been free to change him in some material way to make his death matter, and that would have been a cool mystery. Was that Coulson? Is Coulson still Coulson? While the show tried to have that mystery, it couldn't because Coulson being Coulson was part of the selling point. To me, when I saw Coulson was going to be the lead, that's when the show died to me, and I don't know that I ever really got into it, even though I've seen every episode, that was more out of brand loyalty. I'm also a bit biased, since most of my favorite shows that took dips in quality did so because they didn't know when to let go of characters, because they liked the actors, even though recycling those characters whose plotlines were complete brought the show down, they liked the actors, they liked the characters as they were in earlier seasons, even if those versions of those characters weren't the best for later seasons. Agents of SHIELD started out by centering on a character whose storyline was super-satisfactorily complete, because people liked the actor, and that, imho, was the very first nail in the coffin.
I could go on further about how the show was run, both in missed opportunities and characterization that I just didn't find compelling at all.
And no, Matt wouldn't punch him in the jaw because he's not Wolverine. Matt is not a *****ebag or an a-hole. He would treat Coulson with respect, possibly keep him at arm's length, but he wouldn't punch him in the jaw for no reason.
Yeah, if Coulson comes in all-a-threatening, it's unlikely that Matt will give him any more respect than he does anyone else who threatens him just because they can. Coulson ain't Fury. And if Matt's having one of his characteristic bad days? I dunno, Coulson might just end up face down on a rooftop somewhere.