Lengthy north-south intercontinental routes in pretty much the same time zone, like Europe to Johannesburg, just do not work commercially for daylight flights. USA to Argentina/Chile is another. The flights takes literally all day and thus cannot give sensible onward connections at one or maybe both ends. By the time you have transferred and are ready to check in again, onward services have typically stopped for the day.
It's not only aviation connections, late arrivals can find that onward public transport is finished for the day as well.
There have been a couple of attempts over time, generally where the operations side have managed to muscle over the commercial team, and they have always ended as disasters for revenue. If you manage high theoretical utilisation but the passengers don't want it, what's the point ? The only thing a European carrier can do is leave Europe as late as practical, and try to be back home as early in the morning as possible, after two nights away, to merge the scheduling with other routes. Bear in mind that the bulk of aviation costs are actually related to flying hours, costs which are just straight time-dependent are a minority - this even applies to an extent to aircraft leasing costs.