Hi Wim,
We have spent the last couple of years touring Southern Africa.
I sense you're expecting people to say too much distance too little time? But it's true. I know you're probably thinking you don't want to miss anything but you will get more out of it (I promise) if you cut down on your driving. There is a risk with some bits of your itinerary that you will arrive somewhere late and have to leave early and won't end up seeing much at all. Plus this is Africa and things don't always go to plan. This is a once in a lifetime trip, make sure you enjoy it.
4WD v. 2WD. Well we live out of our Land Rover and need to be able to rely on it so I am biased but be aware that your choice of car will have a huge impact on where you go. You don't necessarily need a Defender/Land Cruiser, or even 4WD necessarily, but for some of the places you want to go you'll need a good strong vehicle with good clearance which will bump up the rental cost. You are also going at the end of the rainy season and you are likely to get mud in any parks and off main roads. We were in Botswana this April and it was quite challenging going in our Defender. When weighing up costs bear in mind camping can offset accommodation costs and opens up some spectacular places.
Looking at your itinerary: Chobe River Front - I would say you need a "real" 4WD, especially at that time of year Mahango you can transit in a 2WD but to drive along the river where the animals are you'll need good clearance, Makgadigadi you will need good clearance, Hwange is a challenge for a good 4WD! In fact in my view you can't really do any Botswana/Zim parks without at least very good clearance and some confidence off-road and ideally 4WD. Of course you can go on game drives (easy to arrange from Kasane for Chobe or Planet Baobab for Makgadigadi or Nxai ) and that may be the answer. I'm not sure what you're thinking of when you say "local 4WD". Doesn't this just amount to hiring a car? Etosha you could do in a tiny car.
Easter holidays - Botswana and Namibia will be busy during South African school holidays - suggest you check exactly when these are. In fact I would suggest you ring a few places now and check out what's available. I was in Maun in May trying to make bookings for parks and June, July, August and September were all full except for the odd day here and there. You could take pot luck, but on your schedule you don't want to be chasing around trying to sort stuff out.
Kruger - haven't done a walking trail but have heard good things.
I would definitely go from Windhoek. Better deals on car hire and easier to do a good circular route. Do Cape Town another time.
Other comments on your itinerary:
The only good thing about Lamberts Bay in my view is Muisbosskerm (the open air restaurant) but I don't think you'll be able to get there as it isn't open too often that time of year. If you want to stop in the area look up Donkieskraal which is great fun - you stay in a very nice converted cave.
This may be contraversial but I don't think Fish River Canyon is so great. The walk would be spectacular but if you drive in, you get to the viewpoint , take some pictures and that's about it. If you do go and you want to camp see if you can stay at Horse Shoe Camp on the lip of the Canyon (it's a Gondwana property that they usually use for their luxury mule trails but they let private travellers stay there if it's not being used). Amazing as long as you aren't afraid of heights. I thought Hobas was fairly crummy I'm afraid.
I wouldn't stay at Luderitz, rather stay at Aus (Klein Aus Vista if you camp). Spectacular scenery and lovely to see the wild horses. Kolmanskop is great but an easy drive (100km) from Aus. You don't need to stay in Luderitz.
Sossusvlei is a must but my advice is to see the dunes in the late afternoon. Morning is a scrum of vehicles and people and the light is just as good at the other end of the day. Accommodation is always a problem around here - even camping is very pricey - but I would go to the Desert Camp - good value and a stunning spot.
Swakop is useful for restocking but not much to entertain you there. Wouldn't call it a highlight and Walvis Bay less so. If you do stay there though do a Living Desert Tour - fascinating. If you're camping rather stay at Spitkoppe (c. 100km away towards Etosha) - amazing. If not camping, I would head for the Erongo Mountains (a little further on your way to Etosha) rather than Cape Cross.
Etosha is brilliant (and certainly if you're in a 2WD will probably be your most rewarding game viewing). Stay as long as you can. The rest camps aren't great but the waterholes at the camps (or at least at Okakeujo and Halai) are fantastic. Take your bottle of wine in the evening and watch the action unfold.
There are a wealth of places to stop south of Divundu and personally I don't really rate Ngepi unless you stay in a tree house which is quite expensive. Mahango isn't worth a day given your itinerary. It is pretty but tiny and not much game (great to see Sable and Roan though). If Etosha is a 9 out of 10, Mahango is a 2. Rather push through. In fact why not stop on the panhandle and do a mokoro trip from there. That's where they'll take you from Maun anyway. Look up Guma Lagoon or Sepupa Swamp Stop.
I love Discovery B & B in Maun. Beautifully decorated traditional rondavels and great hosts.
If you want to do a game park along the Maun - Nata road I'd go for Nxai (if you're camping). One of our favourites in Botswana. Lion and elephant in the campsite on our last visit. You can do a fabulous overnight trip out to the pans (get there on quads, sleep in a bed roll under the stars) from Planet Baobab.
You'll need a 4WD to go through Chobe, though you can stay in Kasane and go on a drive/river cruise. Buffalo is closed but you can drive through to Livingstone.
Again I think you'll need a 4WD for Hwange (our friends had a bad time in their Discovery a couple of months back).
I haven't traveled the rest of your route.
If I were you I would let your vehicle dictate your route. You can still have a fantastic time in a 2WD and if you skip some of your stops you will get more out of the other destinations. You will have a fantastic trip!