tanzania is one of the most commercial countries in the region. the majority of organised tours cost much more than in south africa. the ngorogoro crater and serengeti are usually sold as twin tour packages. if you do goto tanzania be sure to goto zanzibar, its beautiful and the diving is great.
my advice is to pick one safari cause you will see largely the same animals in all parts of se africa. kruger is commercial yes, but its still good. you can goto kruger in a rented car if you like, which is alot of fun. having said that a good guide can be invaluable. the dry season is better for spotting animals when they congregate around water sources. the season you go in will also determine the amount of fellow tourists you encounter, ie - european/american holiday time is packed.
if you really want a non-commercial holiday destination i recommend the ocavango delta in botswana. u camp in the delta and have to be pushed in (by a bloke with a pole) via mocorro (long boat). you dont see as many animals as you would in kruger, although u do see them on foot... but the landscape and overall experience make up for it. also the flight over the delta is amazing.
if i was you id do a tour taking in kruger, the ocavango and victoria falls in zimbabwe. chobe NP in botswana is also very good. and while youre in the region, uganda is an amazing country. kampala is the only capital city i enjoyed in africa, and with activities like rafting the nile, and sites like murchison falls and the mountain gorillas in the south west of the country uganda is simply awesome.
if you dont like commercial, do not goto egypt. as for the masai mara.. when you've got "genuine masai tribesmen" asking for money for a photo of them in traditional dress, then you see them 30 minutes later in used american brand tourist clothing it doesnt really scream non-commercial.
africa is a fantastic place, make sure you mix with the locals at every opportunity cause more than anything else, africa IS it's people.