Units on 25mm bases tend to be tougher. Units on 20mm bases tend to be cheaper.
You can pack 6 20mm bases against 5 25mm bases, without the potential 6th 25mm base being able to fight. This adds a little bit effective value (attacks, wounds) to the 20mm based unit.
Basic size small regiments (5x4) of 20mm might be marginally more maneuverable. Hordes of 20mm are more maneuverable.
25mm are more resilient against template weapons.
-Z