Part of the problem is that most cities in Africa are quite far removed from Rome. Thus, you'll suffer substantial distance to capital penalties. Even for Lepki it is 40%, and for Egypt it will be 80% (the max), unless you move your capital from Rome to a place that is substantially closer to Egypt.

Another problem is that cultural penalties will be quite high too, no matter whose territories you take over (that is because Romans have a unique culture slot). Upgrading governor's buildings (if possible - if you conquered Kart-Hadast after 255 BC, chances are it already has the biggest; same applies to Alexandreia), marketplaces, etc. will help to reduce those penalties. But that will take years, possibly even a decade or two to achieve.

Good governors with high influence can help, but once they die or leave the settlement morale will collapse. And while a Type-4 government lets you recruit a local ruler, they are quite expensive. Furthermore Type-4 governments restrict the options for infrastructure development, meaning that it may be hard to get rid of the culture penalties. Unless of course you'd tear down most of the buildings that provide these penalties, but that is really restricting on your economy.

Distance to capital penalties in Greece are far lower and local recruitment options tend to be decent. In addition to that, distances between provinces are limited. It really helps that you don't have to march your armies for 3 or 4 seasons just to get to the next settlement. Which can be a bit of a problem in Africa as well.

Ideally in the case of trying to conquer Egypt, you have a presence in Asia Minor. Just to keep the supply lines reasonable.