The classic, and most common route would be the east coast.
The reasons for this are many, but along with the usual countries that people are most aware of (eg. Egypt, Kenya), many are surprised to discover places like Sudan and Ethiopia that they may not have known much about but find to be destinations in their own right.
The west is enjoyable as well, though due to a host of reasons it is less travelled, a bit more rough and tumble, and in general less developed. Visas can also be more of a pain to organize.
In general, I would suggest that you can't go wrong with the east coast route for first time visitors to Africa. If you want more adventure, you can always do the west coast route on the way back or for your next trip.
Have a good ride.