I voted BOTF as closer to an ideal type although it would make games even longer and computer resource hungry. (and I like marathon now)
The Civ5 system might be the worst I would imagine although they did bring in the concept of limiting numbers of units based on resources. That, in itself, is a good idea. Likewise, further points made above regarding the logistics of large stacks and marching through tough terrain such as deserts are well made. Some kind of attrition vis-a-vis terrain equation could be brought in with units declining in tough marches and needing to heal afterwards. Healing itself should not be so costless. Essentially, anything that leads to ridiculous abilities or situations needs to be addressed.
The Civ4BTS system with logistical and resource limitations, less emphasis on siege and artillery and some other modifications could be a good compromise. Once there were more limits on the massive stacks and unit production, another experiment could be a morale rule in combat by which a losing defender is not necessarily destroyed every time. Rather, it could break-and-run, possibly losing XPs if it does.