You probably only have one giant flywheel, as the mass is where the energy storage gains make it worthwhile. Maybe you have many of them in parallel, but the size would make scaling an issue. Not to mention that there’s an associated drivetrain and linkages and so on. It’s a fully integrated contraption. It works, but many parts must work in tandem for it to be so.
This is in contrast to an electronic system, which would benefit from miniaturization and isolated redundancy. Racks of capacitors could run as hot spares when energy is abundant next to racks that may be down for maintenance. I doubt that a flywheel can be meaningfully inspected, let alone repaired or upgraded while operating.
That is the benefit of a modular approach to certain problems and not others. The two approaches are not always mutually exclusive either. Capacitors could be used as regenerative brakes for flywheels, for instance.