Hi Pollydill - although I have only been to Tanzania of the destinations you are considering, I am planning a trip to Rwanda and Kenya right now. Others with more direct experience can comment, but to me your itinerary looks very rushed for the amount of time you have. If you can't extend the time frame I think it would be better to visit Rwanda and then Tanzania OR Kenya. You may be able to catch some of the migration during June in the mid or western Serengeti.

Thanks Catey,
I think you are absolutely right, however I don't know if I will be able to visit Africa again. Maybe I will have to add a couple of days?

We all think we are taking a "once in a lifetime" trip to Africa. But then you get hooked, fall in love, and immediately start planning your next trip to Africa as soon as you get home

Given the time of year you're looking at, I'd suggest forgetting about the Mara and concentrate on Tanzania. The Mara is the upper end of the Serengeti ecosystem and, at that time of year, the Migration herds will most likely be in the central Serengeti or the Western Corridor as Cateyes555 suggests.

If you spend the night in Kigali, you can take an early morning Rwandair flight to NBO, then a Precision Air flight to JRO, arriving before noon. I'd add a couple of nights at Tarangire NP. Even at that time of year, it's a great location (eles and baobab trees.) Then, continue on to the Crater, spending one night there (Sopa is a good location on the rim) and do the allowed half day drive the next morning. After lunch, continue on to the central Serengeti (Seronera area.) Spend your remaining time there and fly back to Arusha for your trip home.

Thanks ShayTay,

That is very helpful. I was thinking the Mara should be somewhat similar to the Serengeti.

This maybe foolish, but I would love to see Kilimanjaro as a backdrop for (lots of )elephants, and it was my understanding it was best viewed on the Kenyan side. Is it ridiculous to take a couple or 3 days to visit Amboseli since we are likely overnighting in Nairobi perhaps twice? In other words, will we have to pay the entry fee anyway?

I hope this is not my last trip to Africa, but in case it is....

Hi Pollydill,
You are right that Masai Mara and Serengeti are actually on the same ecosystem presumably similar wildlife and scenery.Since you are interested in Mt.Kilimanjaro then you will have to visit Amboseli National Park in the shadows of the mountain for classic views.The itinerary need to be as below;
1st Night; Nairobi or you may connect an onward flight to Kigali depending on arrival time in Nairobi.
2nd -4th day;gorilla treks in Rwanda
5th Day;Kigali-Nairobi.flight
6th Day;Nairobi-Amboseli-by road.
8th Day;Amboseli-Arusha-Serengeti. flight
10th Day;Serengeti-Ngorongoro.Road
12th Day;Ngorongoro-Serengeti-Arusha-Nairobi.
13th Day;Fly back home

I think this should be an option although there is much flying.
Cheers.