My favorite seasons

I am going to go with:

1. Season 4—Largely driven by the last nine episodes
2. Season 3
3. Season 5—Tentative
4. Season 1
5. Season 2

The last two seasons are practically tied. The weakest first season episodes are worse than the weakest second season episodes, but the best of the first season exceeds the best of the second season.

The final ranking for the fifth season will depend on the final 12 episodes and the extent to which the first ten episodes tie in with the rest.

Given that we are only ten episodes of the fifth season, it might be fairer to rank based on pods. If we define the pods as:

The Beginning (1.01-1.09)—Stand-alone episodes that introduce the show and drive away those with short attention spans
T.A.H.I.T.I. (1.10-1.15)—Deals with the mystery of Coulson's resurrection with a few stand-alone episodes mixed in
The Fall of S.H.I.E.L.D. (1.16-1.22)—Setup and fallout from the Hydra reveal
Hypergraphia (2.01-2.10)—Deals with Coulson's crazy writing
Inhumans (2.11-2.22)—Skye has a new identity while some characters (e.g., Mack, Simmons) have a new prejudice
Maveth (3.01-3.10)—Deals with the fallout of Simmons's vacation, also the ATCU and Ward recreating Hydra
Fallen Agent (3.11-3.22)—WHO! WILL! DIE! Also, the team deals with Hive
Ghost Rider (4.01-4.08)—A flaming ally helps the team defeat Eli Morrow and a few ghosts
LMDs (4.09-4.15)—Mack's nightmare come to life
Agents of Hydra (4.16-4.22)—Fun in the Framework
2091 (5.01-5.10)—Everyone has a nice vacation in the future

I would rank them as:

1. Agents of Hydra
2. Maveth
3. The Fall of S.H.I.E.L.D.
4. LMDs—Redeemed by the last two episodes
5. 2091—Again tentative
6. Ghost Rider
7. Fallen Agent
8. Inhumans
9. T.A.H.I.T.I.
10. Hypergraphia
11. The Beginning