Here is the list of the shoes worn by Eliud Kipchoge over his Marathons
(*) marks a custom shoe
2013:
Hamburg
-Nike Zoom Streak 4
Berlin
-Nike Zoom Streak 5
2014:
Rotterdam
-unknown shoe
Chicago
-Nike Zoom Streak 5
2015:
London
-Nike Prototype v1* (precursor to the 4%, hidden under the pretense of the Nike Zoom Streak, Running Warehouse even reported this after the US Olympic Trails )
Berlin
-Nike Prototype v2* (famous for the soles coming out of the shoe, also has a different lower than the Nike Prototype v1)
2016:
London
-Nike Prototype v3* (Nike Zoom Streak LT2 upper with a substantially thicker sole than the Nike Prototype v2)
Rio Olympics
-Nike Prototype v3* (Nike Zoom Streak LT2 upper in OC colorway)
2017:
Breaking 2
-Nike Vaporfly Elite* (a Next% prototype with an almost identical lower with a fly knit upper)
Berlin
-Nike Vaporfly Elite* (a Next% prototype with an almost identical lower with a fly knit upper, a different colorway than the breaking 2 shoe)
2018:
London
-Nike Zoom Vaporfly Elite Flyprint (technically not a prototype, but it shares the Next% lower with different sole)
Berlin
-Nike Next% Prototype* (Lower is the Next% but with a custom fly knit upper)
2019
London
-Nike Next%
Ineos 1:59
-Alphalflys* (you can find the patent if you want to)
As you can see the 4% was actually never worn by Kipchoge over his marathons, he went straight from the 4% prototype to the Next% prototype.