This may not be a popular opinion, but I don't see anything wrong with the op's plan to split the trip between the two regions. We do it all the time. For me, I figure by the time that I navigate an airport and get on a plane, whether I'm on a flight for an hour or for four hours really makes no difference.

We aren't travelers who need to see a specific country in super detail, but rather we go to places to see what we want to see, following which we split. We love going on safari to East Africa and then heading to CPT or elsewhere in S Africa on the same trip.

Just a few months ago, we went from Djibouti to Rwanda to Kenya to South Africa over a 3-week period. As long as one does careful planning with flights, it can work out just fine. Of course flights can get mucked up, but for me that's not reason enough to avoid someplace I really want to visit on a specific trip. Different strokes for different folks.

FWIW, we enjoyed Rwanda, but for us it wasn't the life-changing experience that some seem to have.