When people talk about the final villain, do they mean the last true single villain to be defeated by luffy or the last great obstacle to overcome? From what WB said, the one carrying Roger/Ace's spirits will end up causing a war with the world (WG?), which to me points to the WG (and it's strongest member) being the very last obstacle for the crew to overcome. Since the war was foreshadowed to happen once a new pirate king appears, so it sounds like it would have to happen after Luffy and BB face off for the title of PK. Unless BB starts the war prematurely after gaining access to an ancient weapon and attempts to conquer/challenge the entire world, which would allow Luffy to fight BB as the final villain while dealing with the WG, and gain the title of PK.
I personally believe BB is the greater villain compared to Akainu, both have been known to use dirty tricks, but I believe BB will take the series to a much darker place more towards the end. Whether the darkest character (BB) would be saved for the very last fight, or the darkest event (the war) is saved for the last fight, I can't be too sure.
If we compare the theory to bleach, arguably the darkest character (Aizen) was defeated half way, while the darkest event is happening at the end. So it's not completely unheard of for the most evil character to be taken down unexpectedly in exchange for an overall more dramatic event.