That implies other causes (which you yourself mentioned above) are minor by comparison. Surely this was true in the 1960s, 1970s, 1980s. But now, 50-60 years later, that explanation alone just doesn't cut it. A lot of places were colonized outside of Africa too, often much more brutally than many parts of Africa (whose colonial legacy is as heterogenous as other things you mention), and are on average doing better (hence the ugly 'poor man Africa' caricature this piece lampoons so well). And yet the onset, length or brutality of colonization doesn't seem to coincide well with stability or quality of governance. Heck, Ethiopia almost got away with not being colonized at all.
Like yourself, I don't know what to prescribe. I do know that it should be Africans themselves doing the prescribing.