The complaints on the site generally criticize Jira from a technical standpoint, but it's important to realize that every "technical" shortcoming is based on a perceived organizational need: you never need the feature just for the feature itself.
So yeah, Jira is far from my favorite software -- it's bloated, slow, and embodies many product choices that make no sense to me -- but it's also possible to hate it because it doesn't support in exactly the way your organization has been doing it since you were working with spreadsheets, and that's not Jira's fault.