I've been binging past seasons over the holidays and wanted to share my thoughts. I will try not to go into tl;dr territory.
I think the first season gets kind of a bum rap. Despite the episodic/procedural nature of the first half of the season, I find that there is a lot about the early days that I miss. The close-knit nature of Coulson's team. The Bus. Big SHIELD, and all of the various facilities (The Sandbox, The Fridge, The Hub, etc), even good-guy Ward.
There were a few clunkers (0-8-4, FZZT, Repairs), but the characters were strong right off the bat. Fitz quickly became the show's most quotable, and by the end of the season, most heroic characters.
The mystery of Coulson's resurrection could have been handled a little better perhaps, but I was largely satisfied with the outcome. Knowing that Centipede was a cover for HYDRA gave that thread more of a sense of urgency and dread, and I enjoyed the various episodes that pushed that thread forward (Pilot, Eye-Spy, Girl in the Flower Dress, The Bridge, The Magical Place).
The second half of the season is when things started rolling. From what started as a fun adventure in TRACKS, turned dark by the end with Quinn's shooting of Skye, marking the beginning of the show embracing its darker tendencies. From there, it was just a snowball growing larger as it went down the hill. The hunt for the Clairvoyant, the rift between Coulson and May, the ascension of HYDRA, the betrayal of Ward and Coulson's team going underground to seek out justice made the second half of S1 a wild ride.
The finale, while almost a little too "Whedon-y", was a lot of fun. Fitz's heart-breaking admission and sacrifice, Fury's nick of time arrivals for Simmons and later for Coulson with the Destroyer gun ("I know what it does"), the final fate of Garrett, and Fury handing over SHIELD to Coulson were all great. Although, upon re-watching, it's painfully obvious that Samuel L. Jackson and Bill Paxton were never on set together.
Random thoughts-- I want to see Akela Amador again. Whatever happened to Ian Quinn and the gravitonium?
The second season built on the first in almost nothing but good ways. The new agents, the larger scope and the introduction of the Inhumans were all organically and smoothly accomplished. New characters like Bobbi, Hunter and Mac fit right in as they've always been there. The death of Tripp was emotional and dramatic.
The "real SHIELD", Cal, Jiyang and the Inhumans of Afterlife all provided exciting dramatic adversaries for our heroes. The only let-down on the bad guy side was perhaps the anti-climactic death of Daniel Whitehall.
Random thought-- What ever happened to the Koenig brothers?
The third season is the only one that I consider a bit of a stumble. The show was already struggling to justify Ward's continued existence in S2, and by S3 he had just about completely worn out his welcome. I didn't really care for the secret history of HYDRA or HYDRA's convenient connection to ancient Inhumans. There were too many threads that built up to disappointing climaxes (Secret Warriors, Werner Von Strucker, Lash, even Malick) for it to be that satisfying in a re-watch. There were some things that I liked-- Daisy's comic book look and the introduction of Yo-Yo and other Secret Warriors elements.
Random thought-- Bring back Deathlok!
So far, season four has been great. Shifting the story away from HYDRA, Inhumans and Ward, along with the new status quo at SHIELD, gives the show a new, breath of fresh air kind of feeling. Also helping in this feeling of renewal is the new focus on mystical threats and AI, which, as mentioned is a welcome change from HYDRA, Inhumans and Ward.