Though they have payroll, they do not pay your taxes for you (only in a few select states). You need to do it manually...and at times I've forgotten and had to pay penalty. Now I use square - and they do it all automatically. I didn't know I had to 'turn off' payroll in wave and was charged the $15 a month even though I didn't run payroll for any employees.
Payments...their recurring invoices are good, but you need to do some manual work. They create the invoices and it adds to your sales. When they deposit your money to your bank it adds to your sales as well. So you need to find the one they deposit and manually delete. I asked if there's like a report they generate that tells me everything they've deposited...it doesn't exist. So you could mistakenly delete something, or forget to delete something...and it throws everything out of whack. You could be underpaying or overpaying taxes.
Their 'ACH' requires people to log into their bank. I'm not going to try to convince my customers to click on a link on my invoice and put in their bank credentials.
I have other gripes...there's definitely room for improvement. I haven't seen that much changed in the last few years...not sure if they cut back on their development team or what. I probably should have looked more heavily into Quickbooks since that's the industry standard. I will look into pilot, though.