The two potential endgame enemies for me are :
1. The WG : They are strong in theory, but i hardly can see them as a final villain on the offensive because they have to much to protect. However, if they had to defend someplace like Mariejoa they could pack a mighty punch in spite of possible internal divisions. The marines are a thing, but we can assume that they would not be the only force at play : CP 0-9, national armies of member states, World nobles may possess personal troups or warrior slaves, maybe some shishibukai if they still exist by then , ect.
Depending on the strength of the unknown variables, they may be a worthy "final" villain. Heck, "One Piece" may even be needed to defeat them, hence the need to defeat BB.
2. The BB pirates : In a way, they where introduced in chapter 1 though Shanks' wound. They're the perfect match for the SH, in terms of symetry. Furthermore, they are more "evil" in a way. While the marines and maybe even the WG can, and probably will, be reformed. I mean, the marines have their good guys and the WG have a few friendly royal families plus the revolutionnaries… On the other hand, the BB pirates are all portrayed as scumbags, they seem to need be crushed.
Only problem I have with this setup is that they are not that theatening for now compared to the combined might of the WG. Furthermore, if the WG is defeated at this point, they may become allies of sorts against BB, unless they have to recover of course.
However, they are growing strong, capturing DF submitting islands, etc. Furthermore, BB has a knack for chaos and I can very well see the SHs actions in the new world ultimately profiting to him...
Finally, if the SHs are occupied else where, the BB pirates may even find "One piece" which may or may not raise their threat level.
To conclude, I feel that BB pirates make a more likely scenario, the only bemol being that they would need major hype to make them credible enemies once the WG has been defeated. However, many things may contribute to that hype:
-Murder of Shanks and maybe Mihawk
-Accumulation of powerful DFs
-Ancient weapons ownership
-One piece acquisition
-Profitering from power vaccum created by the SH's actions
-Ect.?