Firstly, as the continuation of the mysterious alien carvings leds to an intense revelation, the sub story of the team following Ward around on various buses felt to be pushed aside but I presume that the two stories are connected in some way.
I've been trying to pinpoint Ward's obsession with Skye and what he hopes to achieve by terrifying her. I don't think just killing her is his style. He's such an unpredictable character that makes him a very powerful element to the story.
I think the team could have been a bit more conspicous when they are trailing after Ward. I just don't think a cap, a cowboy hat and a book that isn't actually read is going to fool him. Clearly, it didn't- he was wearing a bomb.
The visual effect alongside the direction of the scene where Coulson finds himself back inside the memory machine was really atmospheric and electrifying.
Finally, we discover what these carvings mean- it's a city! An alien city? A another universe city? A city filled with other superheroes or villians? I can keep speculating but that's the beauty of this show, it literally could be anything.