@Aleron Ives - I think you meant to say disassembly. Decompilation generally attempts to translate assembly or machine code into some higher level language, and can be used to reconstruct source code (to varying degrees of success). Disassembly just breaks down the code into assembly opcodes and mnemonics. Disassembly goes hand-in-hand with emulator debuggers, and Dolphin has a disassembler, naturally. It does not decompile the PPC code back into whatever language it was initially written in (C, C++ I guess), although it recompiles a lot into x86 and ARM assembly.
@OP - Your best bet would be learning PPC assembly and how the GC works. If you know what to look at, say whenever a texture or polygon changes in a certain way, you'll know where to look (e.g. checkout what code is updating the relevant registers that are responsible for that behavior). Obviously that's a lot to learn, especially if it's just trying to make a fangame. All the time and investment you spend becoming a console hacker would probably be better spent carefully observing Paper Mario and coming up with your own methods to recreate them. The walking animation for a Paper Mario game is definitely not as simple as it would be in other Mario fangames, but not impossible to do it.
@OP - Your best bet would be learning PPC assembly and how the GC works. If you know what to look at, say whenever a texture or polygon changes in a certain way, you'll know where to look (e.g. checkout what code is updating the relevant registers that are responsible for that behavior). Obviously that's a lot to learn, especially if it's just trying to make a fangame. All the time and investment you spend becoming a console hacker would probably be better spent carefully observing Paper Mario and coming up with your own methods to recreate them. The walking animation for a Paper Mario game is definitely not as simple as it would be in other Mario fangames, but not impossible to do it.