Olaf the Stout
Hero
1. Cross-referencing monster/NPC stats. I know others like them (and they are fine if you know the system inside out), but having to look up several spells, feats, or even common abilities is a nightmare for keeping combats fast. (Case in point - I bought PF Beastiary. Looked at my good old fav, simple orc? Two powers I did not know. 1 was 'Light Sensitivity', with no description, so I look it up in the back and it tells me orcs are dazzled in bright light. So I find Dazzled in the massive core book. It turns out Orcs are -1 to attack (I think) in bright light. Why not write that in the original statblock? Would have been shorter. Anyway, broke my own list rule, will create thread if others wish).
Even worse for me was some of the spell cross referencing. From memory Shapechange was the worst offender. The spell description was quite long and would tell you it worked just like Polymorph apart from (several) differences.
You would then look up Polymorph, which also had a long spell description and would tell you it worked like Alter Self apart from (again) several differences.
At that point, you would look up Alter Self, see the lengthy spell description and just find another spell with a shorter spell description to cast!

It would be funny if it wasn't such a nightmare to try and deal with during play. At the very least they could have told you what page the spell it referenced was on.
Instead you had to madly flick through the book to find it. The spells are in alphabetical order, but it still took time that could have been saved with a page reference.
The other thing I would add to this list is indexing. A lot of the 3.x edition books did not have an index in them. Those that did were often quite lacking. A good index is a godsend when you need to find something quickly in a game.
Olaf the Stout