It’s dangerous to ride a near empty or empty jeepney. Several things can happen.
One, the other passenger might disembark before you. Thus, leaving you alone. If you’re alone there are several things that can happen. The jeepney driver might cut his trip and transfer you to another jeepney or he could just return your fare and drop you in no man’s land!
The other scenario for a near empty or empty jeepney is that the driver would stop on each corner and wait for several seconds for potential passengers. Imagine the cumulative delay that you would encounter. At least you would still arrive in your destination, although minutes late.
So choose not the empty or near empty jeepneys. It’s for your own good!