They are very different - hard to compare.
Jiko is a fine dining establishment. Very neat atmosphere, top notch service (typically), excellent chef created dishes, huge African wine list, quiet and laid back.
Kona is a hotel lobby restaurant. Great food but not fine dining, good service, lobby atmosphere, find for families and children, not quiet and laid back.
I love both. If I want a night out with my DH, we would head to Jiko. If I wanted a place to eat before hitting the MK in park attire, I'd pick Kona.