Humanoid harem - Kissing makes them stronger
Probably Sekirei. 


  the story was about humanoids


Which are called "Sekirei".


  All the humanoids were girls 


Most, but not all (Shiina is male; Homura may also be). Equal-opportunity fanservice!


  the main character 


Generic McProtagonist-kun.


  helps a man and his humanoid escape the city


Shigi with his Sekirei, Kuno.


  the main character's sister had a humanoid that was trying to find her sister which was the main character's humanoid


sister = Yukari; her Sekirei = Shiina; Shiina's sister = Kusano; Kusano's "master" (Ashikabi) = McProtagonist-kun.