@michel: that is in fact a good argument. of course we also think about transportation of goods, but the question is whether subway systems will be the future as they are pretty expensive. Furthermore, goods take less space and don't ask for flexibility (like people). So they might either be shifted to the current subway systems or remain overground.
@xittenn: Sky city indeed is a very interesting project. That would be the opposite approach: decreasing the need for mobility by making buildings higher. The major problem is the weight of such high buildings and of course the danger that an emergency in just one building might endanger the lives of several thousands or even hundred thousands of people. Furthermore, money also plays an important role. We are really looking for feasible solutions but e.g. sky city would cost several billions. Could be an option for very rich countries, but with millions of inhabitants in future megacities there will also be a lot of poor people. They won't be able to afford such housing.
@ewmon: you are right with questioning the assumptions and of course, different developments have an effect on the actual solution. With mobility becoming a major problem (a lot of time is spent in traffic) and job opportunities more and more to be found in cities, urbanization is quite a good assumption in the first place. With more and more people moving to cities and even slums becoming overpriced, many people might move back to rural areas. Tackling urbanization does not seem to be of any "stakeholder"'s interest: people themselves want to move to cities where there is a better health service, more job opportunities etc.; governments would need to invest a lot more in public transport if people need to travel longer distances. And harvesting might be done only by machines.
Probably future transport might be a mixture of what you mentioned: Multi-person units for the majority of the distance and single-person units for the so called "last mile". Flexibility seems to be one of the major problem areas as flexible public transport is very expensive (i.e. lower frequency etc.). It might be vital to find a good solution for this last mile as this is the major reason why people take the car. As parking spaces are limited, eliminating ownership of vehicles and providing a high-tech on-demand vehicle system could be a feasible option. And I agree that flying vehicles will probably not be the solution within the next 30 - 40 years. However, the higher the buildings (as mentioned above) the more attractive such solutions.
