I can't guess your level of expertise in the topic of IR protocols, so I have no idea what aspect or level of that difference you want to understand.
If you explain why you want to know that, maybe that will give more of a clue of what it is you really want to know.
There is a begginer oriented, but fairly detailed description of various IR protocols, including RC5 and RC6 at:
[Link: sbprojects.com]You could compare those two descriptions to see most of the differences.
