The idea is to rent a car (can be with travel guide - recommended online option) and visit highlights of Madagascar. I've read it's best option to get around. National flights are also an option to save time :)

Places to visit (but I'm flexible):

Antannarivo, Morondava, Avenue of the Baobabs, Tsingy Stone Forest, Ranomafana National Park, Isalo National Park, Andasibe National Park, Ile Sainte Marie & Ile Aux Nattes, Ifaty, Masoala National Park