Alignment has never been a problem for our group; we still use it.
Regarding the original query, I wish they would have put out NPC Codices for the classes past those found in the Core. Having a ready made Cavalier, Warpriest, Investigator, etc of various levels would have been helpful.
Aside from having a straight 1 through 20 of each class, I would have like to have seen mixes such as the NPCs found within the GameMastery Guide or Inner Sea NPC Guide.
Also wish they would have put out a Monster Codex II. I would not have minded additional stat-blocks for those creatures in original MC or new creatures they hadn't touched yet.
A Villains Codex II would also have been welcome.
Edit: apologies if any of these had already been suggested; I did not read through the entire post history.