User interface can sometimes be an issue for some. I believe less is more in most cases. Some times there is too much involved in screens that tend to get people confused.
Having to open multiple screens to complete 1 process, and the lack of standard reporting. If you need reports there needs to be an onsite report building employee, or syspro has to do it for you.
Customer support needs to be more stable. I have noticed that the timing of ticket resolution tends to be a bit long. In previous years we would get solutions to our issues pretty quickly, but recently it takes days to weeks for a response from the support team.
I'm not sure if its out internal infrastructure or SYSPRO, but there are often times where out system is extremely slow. Review collected by and hosted on G2.com.