Aguero even aged is still faster than Kane.Aguero wasn't blessed with pace, especially when Pep came in. What Pep wants in a striker is one who tracks back, tackles, links up the play to the wide men. All things Kane does.
City's period of dominance occured with aguero up top, sterling in form and sane/Mahrez on the wing. It's when they were at their most cutthroat, and it was breakneck speed. Kane central slows them down, like it did when de bruyne played false 9.
I think pep is overthinking it, and trying to build a different system to the one he's had great success with. I think it's his ego.