You don't mention the factor that bears most on this subject. How many people are involved?
If you are talking about 100 persons per "family line", by all means keep them in one file is the best answer. You will get operational efficiencies because of centralized things like place names and common report formats and common sources, etc.
If, however, you are talking about 10,000 people per family line, one might want to keep them separate. This is because FTM gets real slow with a lot of people. I can't really say how many people it takes to get real slow. I would be inclined to put them together and when things start to get real slow consider splitting lines off with the Extended Family Chart.
By slow, I mean the time it takes to:
move to the next field when entering items and hitting enter
The index redrawing itself when switching to the Family tab of the People Workspace
The time it takes for a the cursor to become active after moving to a field.