Great post and I agree with everything you said. I edited parts of it only for the sake of brevity but you really hit every problem AOS has perfectly.
The points you made about Mike Peterson are ones I agree with and have stated before. At the end of the pilot episode I really could not believe that Coulson chose to drag Skye along with his "elite" team while leaving a gifted man with the potential to become a superhero behind. The show would be so much stronger had Whedon et al. been smart enough to recognize the potential of introducing us to SHIELD through the experiences of an Everyman hero whom Coulson had taken under his wing for training. There was still plenty of potential conflict in that setup, as perhaps Mike would object to some of the methods employed in encounters with fellow gifted individuals, or disagreed with some of SHIELD's policies.
But instead of going with Mike, which would have been a brilliant move, they went with the Whedon tried-and-tired strategy of using young female as the show's focus. Mike was brought back, but only so that he could be disposed of in some manner so that the audience will stop asking about him. Either he is well and truly dead or he'll quit SHIELD because he needs to stay with his son, as Coulson strongly suggested. Dead or alive, there will be no superhero or superagent career for Mike in AOS's part of the MCU.
Coulson and Ward should have had an interesting dynamic, especially since Ward questioned his superior's inexplicable decision to recruit Skye. After Skye was exposed for betraying the team, Ward could have stepped up his opposition to Coulson's tactics, furthering the tension between them. That would have been a way to highlight the ways in which Coulson has changed from his old by-the-book way of doing things to a more intuitive style.
I agree with everything you said, but it isn't just Mike that was nerfed in favor of Skye. Ward is in the exact same boat as him.
The Ward we are introduced in the first episode is not the same Ward of the rest of the show. Ward is introduced as an excellent young spy - had the best espionage results since Romanov, was apparently an expert at diffusing bombs, could go in undetected to complete a mission and get out unnoticed, etc. Furthermore, Ward is also initially portrayed as the viewer's eyes and ears from the inner SHIELD world, just like how Mike was the viewer's eyes and ears from the outside world. Everything SHIELD-related is seen from Ward's perspective. We get reintroduced to Coulson through Ward's perspective. We enter the plane and meet the whole team through Ward's perspective. Ward's contrasts with Coulson are also put great emphasis on.
Then from the second Skye gets on that plane, we never get into Ward's head to that same extent again (other than kinda in the Thor episode). The rest of the episode is reduced to a Coulson/Skye teamup and the event that triggers it is Ward being shot with a truth serum by Coulson that turns him into a complete wuss in front of Skye.
Following that moment, Ward also is reduced to just "punch anything that moves" brawn for the remainder of the show - and
redundant brawn, since we already have May and Coulson for that - while every other youngster on the team has a talent there is no proxy for on the plane if one of them goes missing. What the hell happened to "best spy since Romanov"? Only episode we see him doing that is in the one where he fails at it
and gets major help from Skye. What happened to the in-and-out bomb-diffusing expert? Only episode that deals with that is the one where his job was to escort Fitz to Russia so that
Fitz could diffuse the thing only for Coulson to come to their rescue (so much for "in-and-out"

). Also, his far more interesting backstory? Nope. Let's address it every 5 episodes, but let's deal with Skye's backstory in almost every episode.
I should take a moment to make this clear: I don't think Skye is a bad character. I just don't think she deserves so much more of the main protagonist spotlight more than Ward and Mike do because a) she is the least interesting of the three and b) she is the least deserving of it based on her past with betraying SHIELD. She is literally a character randomly picked up from a van that the whole plot now revolves around because "the writers said so".
But of course, I shouldn't be surprised. This is Whedon we are talking about here. With Whedon, it isn't about which character is the most complex or has the most story potential nor is it about who would fit better for the main protagonist role. It's all about who
he likes; that character will be shoved down people's throats, even if more appropriate characters for that particular part need to be ignored/hurt in the process. It should be pointed out this is the same guy who refuses to acknowledge Hank Pym's importance to the Avengers and to Ultron but fought to get Janet as a founding member in the first film.
Whedon is the Geoff Johns of Marvel - a very talented writer but has too much of a hard on for his favorite "pet characters" that he would do anything writing-wise to prop them up, even if it means crapping on other characters.