But in the end, they should have included them - the "everything is just one big list" method is really, really terrible.
I disagree with that. Let's think about seeking information at game time in a step by step fashion. We'll assume the step of finding the section of the book that has the spell descriptions because that's common to all organizational methods and fairly trivial.
Organized by class, then level, then alphabetically
1. Find the appropriate class section in the spell list for the class
2. Find the appropriate level section in the class list by level
3. Find the specific spell in a relatively small alpha section
Notes - this is easier for players who probably have their spells listed before them already grouped by their class and their level than it is for DMs who have to go through the additional process of identifying the PCs class and identifying the right level of the spell in question.
Organized alphabetically
1. Find the specific spell in a large alpha section
While step 3 in the former will be easier and quicker than step 1 in the latter, organizing by class and level first requires more processing of information when trying to access the information at game-time. And
that's when I want the organization of the material to designed for speed of access. A single alphabetic list provides that.
I think the class/level (school) organization works well for character building because it promote browsability, which is very useful when trying to decide what selection to make at build time. But that's generally a time when efficiency of time is less important. It can afford to be a bit less browsable compared to my information need at game time.