I was lucky and got through while the ferry was still running so I'm not sure whether the hassle of Egyptian customs is worth it, but shipping to Kenya you miss a lot out.
If you're just going to ride down the road then give Egypt a miss, but if you want to see some antiquities there's nowhere else like it. Yes it's hot and dry in Sudan but a nice country to visit all the same. And Ethiopia is a bit like marmite, but no-one could deny an interesting experience however you feel about the place.
Going direct to Kenya then south I feel you'll miss a lot of the diversity Africa has to offer. I've no idea how possible / easy / difficult it would be but how about as a compromise going in at Djibouti?
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