Hey there,
I did an episode of the AskHistorians podcast where I talked a little bit about Roderick and Susan McIntosh's digs at Jenne-Jeno. I also wrote this answer where I cover some of the same ground as in the podcast.
In a nutshell, the answers I give there are this: The academic consensus up to then had presumed that African cities in West Africa arose due to the establishment of Trans-Saharan trade, and thus early cities in the Middle Niger should strongly resemble urban archetypes from North Africa or the Near East. However, instead of the nucleated settlements familiar from excavation in Mesopotamia, (i.e. cities with a distinctive "core" with palace complexes/temples/markets, and surrounding residential neighborhoods) instead what was found was non-nucleated settlments. That is to say, separate settlement sites with specialized fishing or blacksmithing, or weaving (etc) economies appear in proximity to each other, and over time these separate sites grow in population and extent to form one single urban aggomeration at Jenne-Jeno. Rod Mcintosh talks more about it in this video lecture. So, these discoveries contributed to already-ongoing debates about exactly what a city is, and what is the best way to conceptualize what makes a city a city.
Another development in the past 40 years of archaeology at Jenne-Jeno and at Gao Saney (I don't think that there has been substantial archaeology done at Timbuktu) has been a greater appreciation of 1) the climatic variation in the sahara and in the sahel over the past 5,000 years and specifically how alternating periods of relatively wetter or drier climate over the past 2,500 years (since Jenne-Jenno or Gao were first settled) have impacted settlement patterns and human migration. And 2) greater appreciation for the regional trade interaction in the sahel-sahara region which long preceded the documented* Trans-saharan trade. Susan McIntosh discusses both of these factors in a really fantastic chapter (chapter 7) in Engaging with a Legacy: Essays in honor of Nehemia Levtzion.