The controller will separate you from all other IFR traffic - by either 3nm or 5nm depending on the airspace, and/or vertically by 1000ft. This may mean you'd get vectored around. Compare that to a VFR clearance where you may get held and told to orbit to keep you out of the way of IFR traffic.
But the main reason you'd want an IFR clearance rather than VFR is because the weather doesn't permit you to make a zone transit VFR.
If you have an IMC or IR you can also make a VFR transit without being in sight of the surface i.e. above cloud.
NS