The biggest gap we see isn't the tax-filing split, most businesses figure that out quickly from Wave's own setup flow. It's job and project costing. Wave Payroll calculates wages correctly but has no concept of which client or project an hourly employee's time should cost against, which matters a lot for a small contracting or service business that bills by project.
The second common pattern: a business running Wave Payroll alongside a separate time-tracking tool because Wave's own time tracking is basic. Getting hours from that tool into payroll without re-typing them is exactly the kind of small, repetitive sync we build.
For businesses in a self-service tax state, we've also built reminders and data exports that make the manual filing step less error-prone, pulling the exact numbers a business needs to file instead of someone re-deriving them from a payroll report by hand.