Acnologia would win , he literally lived centuries and trained specifically to kill creatures like kaido , he has multiple advantages over him like:
1-STRENGTH
Scale to Nastu and Aldron physical strength, was able to break fairy sphere
2-SPEED
Can travel through continents in seconds, fast enough to one shot God Serena ,Gildarts and beat all 7 dragon slayers
3-DRAGON SLAYER MAGIC
Can bypass dragons normal defense , increase his sense like smell, can attack dragons souls and his able to devour every magic
4-DRAGONFICATION
Can transform into a dragon increasing his strength , can fly and becoming much more resistance to everything it's not a dragon or a dragon slayer
5- RESISTANCE TO MENTAL ATTACKS
Can't be controlled by Future Rogue dragon manipulation magic , immune to Cobra mind earing power , can act by instinct if his mind and soul get separate
6-EXPERIENCE
Lived more than 400 years fighting against dragons and dragon slayers
7-CONTROL OVER THE REVINES OF TIME
Have control over a dimension of time/space magic were he can teleport others
Beside how much one side this is , i would love to see a future death battle between this two ( hope they don't screw it like Sanji vs Rock Lee)