AoDOCRH

Advantages of disassembly over compiled-ROM hacking:

Pointers do not need to be rewritten after every time they're shifted, because labels are used instead.
It has all of your familiar scripting languages-- plus much more and no less.
It's far more readable. (Hex numbers or macros? You choose.)
It is in multiple files, not one huge, daunting ROM.
It can be managed properly in git, which has advantages of its own.
You can change whole data structures, like the party Pokémon struct, very quickly and with few errors, which is obviously not something that would be plausible in hexadecimal.

Ask the experts in PRET's IRC channel for more.