To me, having the personalities and clan summary sections AFTER the narrative sections (particularly return to the pentagon) makes no sense at all. I found there were a lot of names in the Pentagon campaign that I had no real context for until I read the personalities section. Adding this (and the section summarising the traits of each clan) between "Building a New Society" and "Return to the Pentagon" would have allowed for the narrative set up of the conditions that gave rise to the clans, as well as providing much needed context for the narrative of the Pentagon campaign.
It's the problem with many of the new sourcebooks. It is best to read them not page by page, but by context: read introduction, then faction 1 story, characters for faction 1, then faction 2 and it's characters. That problem is the worst in Era Reports. I like like they did it in 20 Year Update. Every faction has it's own separate chapter, from the begining to the end.
The layout of the Pentagon campaign section itself was the most jarring. The sections on Circe and Dagda both mention Andery Kerensky's death, which does not occur until the Eden section. Some foreshadowing is fine, but the Dagda section ends with "Operation KLONDIKE was over." Turn the page and you then read all about the Eden portion of the campaign. Additionally, the Dagda campaign required Clans Wolf and Jade Falcon to assist following the completion of their campaign on Eden. I think that the Eden and Dagda sections could have been switched with no rewriting required, and that this would have made for a much better flow to the narrative.
It was written this way, so the most popular Clans - Bears, Jags, Falcons and Wolves - campaigns would be at the end.
Operation Kondike is a really good sourcebook. I would suggest to everyone:
1. Introduction.
2. Exodus and Escalation.
3. The Clans: Children of Kerensky.
4. Personalities (pages 104-121).
5. The Pentagon.
6. Return to the Petnagon.
7. Aftermatch (excluding personalities).
It makes the most sense in that order. There will be some spollers, but it's failry known storyline and makes no real surprises. It spoils itself in the original order anyway, like You said about Dagda campaign.