This idea has been suggested in previous threads and one of the major problems with it is that it post-independence it creates miniature states that probably aren't sustainable.
Here's a map I dug up with a quick search to illustrate. Northern Africa, Southern Africa, and the Horn of Africa look somewhat manageable, Central Africa and the southern part of West Africa would be just a mess though.
Realistically speaking, you are absolutely correct. I do want to point out, however, that a century ago, if you divided Europe by the actually spoken languages, it would've looked the same. 100 years ago, most people in even the Netherlands (a rather small country) typically spoke the regional language. A country
this small had multiple regional languages! Same goes for Germany and many other countries. Although the process was already underway (due to the centralising tendency of states), only the last century really saw the standardisation of language within European "nation"-states. It is theoretically conceivable that Europeans would try to do in Africa what they were (at the very same time) starting to do in Europe: unite an area they consider culturally 'united' or 'similar', determin which language/dialect is the most spoken or most prestigious, and make that the standard language of the region. (But of course, realistically, they'll try to force their own language on the native inhabitants of the region...)
As far as organisation goes, the might be better perspectives. Yes, Africa was a large quilt of relatively small cultural areas. Theorectically, someone interested in creating culture-baed borders could respect those small areas, but unite them into confederations. Essentially turn every colony into a decentralisad amalgation of tribal fiefs, princely states (possibly free cities)... that kind of thing. The small-basis setup for this might also make it easier for some, ah, 'misallocated' fiefs to secede and joing another confederation in the post-colonial period. (I'm assuming that even if this kind of division is done with the best of intentions, there are going to be mess-ups, and mutually hostile peoples are going to be put into the same confederation by sheer European incompetence.)
Although I do not find this realistic (because it doesn't fit with the main motivations of colonialism), it's conceivable that one European power, under an extrordinarily Englightened monarch or so, could implement a policy like this. If it works well, other might adopt (elements of) it. In any case, if done with honest intentions, and assuming all other factors remain roughly equal, I do think this will be an improvement over OTL. Anything that's based on existing tribal fiefs and decentralism is going to be better than
"let's throw 'em all together within arbitrary borders, including people who speak utterly different languages and who totally hate each other, and then have them form a singe central government later, okay?"