Pein and Madara's plans for Akatsuki seem to be in sync so far. Madara and Pein want control of the nine tailed fox as well as the tailed beasts. Pein wants to destroy just about everything,but Madara probably just wants to rule everything. You can't have a kingdom without followers. Eventually one of thems going to have to put their foot down, only one of them can have power like that and Madara dosent seem like the sharing type, and peins probably going to pissed if Madara makes any last minute changes to his master plan nuking the crap out of everything.