Hi Cecco:
My experience doing ferry flights in and out of Africa has taught me the following:
1) Some handling companies are better than others. Often this is as a result of the performance of a single individual at the handler. So, you might want to try a different handler for your next trip.
2) As you have probably discovered by now, some countries are pretty efficient with the permits, and some are not. I have learned to simply avoid overflying the countries that give me chronic permit problems, even if it means a 10 or 15% increase in trip mileage.
3) Familiarity breeds friendship and efficiency. To the extent that it is possible, try to use the same routes and stop at the same places.
Hope this helps,
Michael