Did I mention that this thread will contain spoilers?
What are the weakest books in each of the published adventure paths? (If you know of a fix, please link it.)
Rise of the Runelords: the connection between book 2 and 3 is weak as written, and the GM should orchestrate a bit better the involvement of the PCs with Magnimar's destiny. Even just having some background ties should suffice.Book 4 is a big brawl fest, some groups may not like it. Book 6 is a bit of a sandbox in the eploration of the city of Xin-Shalast, and finding the good rythm between fights and various stuff is not always easy; also it's difficult to manage the loot.
Second Darkness: the first book is plainly... wrong sided. Reverse the plot: the PCs work for rivals of Saul and try to sabotage/investigate the Golden Goblin saloon.
Book 5 is too much of a railroad, break it apart, take the crunchy elements and the general idea and rework it from the ground up.
Book 6 is more a mini-setting than a full blown adventure, you should build lots of thematic encounters and mini-adventures.
Legacy of Fire: book 5 should be an exploratyion of the City of Brass, not being trapped (again!) in another dimension.
Collecting informations, tricks, and maybe an exotic magic item or two by doing favors and errands on behalf of powerful extraplanar beings in an unusual and inherently dangerous place.
Reverse engineer the encounters in many different places instead of a single big dungeon.
Council of Thieves: what demiurge 1138 and Lord Fyre have said.
Serpent Skull: book 3 suffers the same mini-setting and no adventure problem seen elsewhere. Also some players may not like the long voyage in book 2.
Jade Regent: the artic trek part may bore some players to death. Scrap the caravan rules altogether. Be cautious of the large cast of NPCs, they may make encounters too easy or steal the spotlight.
Book 5 should be hugely expanded: building up a national rebellion is in no way doable with an handful of encounters.
Be very, very, very cautious of the ever present narrative chokepoint, in which a deus-ex machina NPC provides the means to go forward in a place/moment/situation the PCs have no other way of getting through (this alone has been the biggest roadblock for me).