When we traveled in May, Mombassa and areas around were seeing an increase in crime (and all that could mean). We took a little vote between the two of us we decided we would avoid that area.
The reason we went to both Amboselli and Masaai Mara was a hope of seeing Mt. Kilimanjaro (which we did see the snow covered top through the clouds) Loads of elephants at Amboselli and lots of "cats" at Masaai Mara.
If you need shorter activities:
I would HIGHLY recommend both the David Sheldrick Elephant Orphanage and the Giraffe Center (both are in Nairobi (Karen). We also loved visiting the Kitengela Glass Factory, also in Nairobi. We signed up for an "experience" and each of us made a glass paperweight. Finally, we went to a coffee farm in near Nairobi (I learned a lot about growing and harvesting coffee beans. We took a walk through the entire place- fields, to drying, to roasting and more.