Mr Light wrote:
It's really unfortunate that they decided to open the series with so many standalone episodes like a vintage 90s series.
But they weren't entirely standalone. They were establishing the characters, introducing ideas, laying the groundwork for things that would pay off later in the season. Let's take a look at just the first ten episodes:
"Pilot": Introduced Mike Peterson, Centipede, Dr. Streiten, "Tahiti" cover story.
"0-8-4": Introduced the idea of an 0-8-4 as an object of unknown origin, and revealed that Skye had ulterior motives for infiltrating the team.
"The Asset": Introduced Ian Quinn; raised questions about SHIELD's dark side; set up Franklin Hall/Graviton for future use.
"Eye Spy": Introduced eye-implant controllers and underlying conspiracy.
"Girl in the Flower Dress": Reintroduced Centipede; introduced Raina; paid off Skye's Rising Tide arc from eps. 1-2 and revealed her search for her origins; introduced Edison Po; first reference to the Clairvoyant.
"F.Z.Z.T.": Showed Coulson exploring doubts about his condition, questioning SHIELD orders; advanced character arcs for May, Ward, Fitz/Simmons.
"The Hub": Introduced Victoria Hand; advanced Skye's search for parents, Fitz's character arc.
"The Well": Asgardian staff had lasting impact on Ward; beginning of Ward/May relationship.
"Repairs": Fleshed out May's character.
"The Bridge": Return of Mike Peterson, Centipede characters; Peterson blown up, Coulson abducted.
So almost all those episodes, and certainly the first five, introduced elements that would be central to the arc later on. They only seemed standalone because we hadn't seen the payoffs yet. You have to plant the seeds before they can blossom.