They built up the entire first season on the mystery behind Coulson's resurrection, more particularly to Coulson confronting Fury about it, only to never address it. All that buildup over how he came back only to get a quick in-a-nutshell explanation about how they brought him back because "[he's] the heart of SHIELD". Which is fine, but that still doesn't answer all the other questions that come with the mystery. We know why they brought him back, but don't know how. How did that blue alien get there? Do they even know it's an alien? How did they figure out they could cure people with its blood?
I'm not expecting all the answers or for Fury to even know what it is, but we should have at least gotten an explanation from Fury's point of view. "In 1961, our scientists spotted a meteor shower and something hit the Earth. We got there and found this blue creature, then discovered we could use its blood for x and y." Something like that would have been enough.
At the very least, Coulson should have confronted Fury about what that thing was. It felt very out of character for him for him to not do that when his whole character arc this season was "no more secrets" and has a protege injected with the same formula! So I totally don't buy he wouldn't have at least asked Fury, even if he didn't give him an answer.
It came off as Marvel saying "Well we don't want to address the Kree in any way yet so we'll just dumb down Coulson a bit for this scene", even though that's the one scene they've been building towards the most since the start. And from the way the dialogue is played in that scene, it feels like they took measures to trick viewers into not questioning it. "I brought you back because you were the heart of SHIELD, and now you will be the head." Notice the conversation shifts instantly from one topic to another. Before people can even make up their minds on the first, their brains have already proceeded to the idea of Coulson rebuilding SHIELD and Season 2. If there was more of a pause in between, I think more people would have questioned it.
By the time we got those Skrull symbols at the end, I just couldn't care anymore. I lost faith in their ability to construct a solid mystery story around Coulson's character. The Clairvoyant mystery was well done and tied into the MCU nicely, but they totally blew all the hype building towards Coulson confronting Fury. Which sucks since they totally sold me with the idea in the second half. Before release, I had mixed feelings on bringing Coulson back. Then in the first half, I wasn't sure if the show merited teasing the process of his resurrection so much. Then in the second half and up till the finale, I totally bought it due to how complex it became.