I like that we have all of our pay periods synced up so it is easy to see if someone has worked more than their allotted hours per week/month without being able to take time off during vacation weeks etc! It would be nice not having an application load when you are trying add new users but this could just mean there isn't much demand at my current employer as they use Paychex already which makes sense given how similar everything seems between them (Deil vs Payshexx).
Also sometimes its hard figuring out what your rate should actually end up paying each month because some months will only cover 1% while others 15%. But overall good product - saves us tons over other services by keeping track ourselves instead relying solely upon HR department who charge extra fees every year since everyone else does too now haha.