Traditionally, D&D had spells for Cleric and Magic-Users (and other classes that used spells in that edition) organized by level, with all spells of first level presented together alphabetically, followed by second level alphabetically, etc.
3E took the encyclopedic approach, with all spells, regardless of level or class, arranged alphabetically in one big list.
There are advantages and disadvantages to both.
In the old setup, it's easy for players to peruse the spells they can access early on and compare them to each other. If all the first level spells are on one or two pages, it's easy to get a grip on them (of course when you get up to 30+ spells as in AD&D it takes a bit more space, but they're still all there together). And as your PC gains levels, you can digest the new spells in manageable chunks. For learning your character's options, it's very convenient to have it this way.
The newer setup, however, also has its advantages. If spell X is listed in a monster writeup, magic item description, or a module, you can look it up easily without having to remember if it's an M-U or Cleric spell, and what level of spell it is. Also, for spells that are on multiple spell lists, they only need to include the text once.
I'm partial to the first way, because that's what I started with, and since I mainly play Classic where there are only 8 or 12 spells per level, it's not that hard to keep track of them all in my head. Despite having played 3E for seven or eight years I never read through every single spell description in the PHB. I have done that with all the spells in BECM (multiple times). I don't remember if I ever did with AD&D but I may have.