First I will rank them according to how well each book in the series actually showcased it's theme villain or Villains, descending from best to worst:
1. Zero-Sum Game- Extremely creative and in-depth look at the Breen.
2. Rough Beasts of Empire- A great bit about both the Tzenkethi and the Romulans.
3. Seize the Fire- We see that there are a bunch of castes and an egg crisis, but not much more than that.
4. Paths of Disharmony- Mostly a cameo by the Tholians.
Pacing:
1. Zero-Sum Game- Quick.
2. Paths of Disharmony- Starts out slow but escalates well, could have done without the multiple paragraphs-long synopses of past episodes.
3. Rough Beasts of Empire- Slow and steady, very much like the novel Dune.
4. Seize the Fire- Felt like being jerked about on a roller coaster.
Characterization (including faithfulness to the original material)
1. Paths of Disharmony- Picard was Picard, Geordi spoke exactly Geordi, etc.
2. Seize the Fire- Similar to the entry for Paths of Disharmony.
3. Zero-Sum Game- Bashir seemed just a tiny bit too comfortable with his secret agent role.
4. Rough Beasts of Empire- I know that it's been said elsewhere, so I'll be brief: there are better ways to make a man independent and "adventure-ready" than this.
Plot
1. Paths of Disharmony- Simply fantastic, loved the ending, could have been a Next Gen episode.
2. Zero-Sum Game- It's 24 in space.
3. Rough Beasts of Empire- It's Dune in space, er, Dune in Trek
4. Seize the Fire- needed a lot more polishing.
Overall
1. Zero-Sum Game
2. Paths of Disharmony
3. Rough Beasts of Empire
4. Seize the Fire