I really think that the main thing wrong with the show is that, with the exception of Greg Clark, most of the actors are simply bad fits for their characters. Only Fitz and Simmons (and Mai to a lesser extent) have any real charisma or appeal to them at all. Making Sky the focus for things was a terrible choice, and Ward's actor is just as bland and shallow as you can get. We couldn't even get a tight smile and a 'Hail HYDRA' from him at the end of last episode. I can understand 'cold blooded, does what needs doing', but he doesn't react to much of anything at all. I'm pretty sure that he's faked his switch but it would be very beneficial to the show if he hasn't - then he'd be gone as a regular.
I'm pretty sure at this point that without Clark, this show wouldn't have made it past episode three.
Part of the problem, though, has probably been things out of their control. Most of the season has felt stiff and disorganized for some reason, and I wonder if that reason is not Captain America 2. I can easily picture conversations like 'We want to do X' 'You can't do that.' 'Why not' 'Can't tell you, yet'. 'Well then our long range plan is Y' 'Sorry, can't go there' 'Why?' 'Can't tell you, plans have not firmed up'. Both TV and movies have such large lead times and yet things can change at the last minute that it might well have been a huge amount of frustration working on AoS and having to dance around what the movie-verse is doing or might be doing. Now here at the very end we have something that could have been done with greater forshadowing all along, and we have a decent Marvel-based villain group instead of 'Centipede' and 'The Clairvoyant'. Though I'm not sure why they could not have used, say, AIM as a know group this season and put them behind some of the goings-on.