This has been the reason bookmarks have existed for ages.
No organization is going to end up working perfectly as we all have our own organization idiosyncrasies. We can fight about it until the cows come home and still not have a good answer. Some want the book for consultation at the table. Others (like me) use it when looking for ideas when putting an adventure together. Others use it like a coffee table book for reading enjoyment, and some simply want it to encyclopedic. And I don't think WotC would make any money if they published five or more book variants to cater to each.
All I know is that the 2014 MM was flawed with putting Beasts and NPCs in their own separate sections, and the 2024 was flawed putting Blue Dragons under B, Blue Slaad under S and Gas Spore under F. Even 2E had issues with the 3-ring binder version when it tried to do it one-monster-to-a-page so the owner could sort it however they wanted. I'm sure you can find a flaw with the 1E version - even if its the fact monsters were being built stream-of-consiousness over three books (MM, FF, MM2).