We finished this AP not long ago after four years of playing and we really enjoyed the ride, though those that played murder hobos had a better time because of the sheer challenge of the baddies.
I think character motivation can greatly help with the weaker points of the AP up to Saventh Yhi. Unfortunately, what motivates a character to gain riches from a lost city doesn't transfer well to fighting underground to save humanity...so I let my first character go after vaults of madness and had a new character come in who had a great interest in the serpent folk.
Our GM just described him and the group took it the wrong way and found him annoying. My group blamed him and the Pathfinders for divulging the secrets uncovered on the Shiv, especially that song he sings.
I am planning to begin this AP soon but did not like beginning in Brinestump. I really want to install more foreshadowing at the beginning, so I thought of doing a 7 Samurai-style start: a hamlet in Varisia is desperate for heroes to protect it from bandits (who have the weapon with the message hidden inside).
The PCs have solid backgrounds in Sandpoint that logically tie to Ameiko and Koya. Shandru is easy and Shalelu is going to encourage the PCs to protect the hamlet from bandits.