One of the things we struggle with is cross repo consistency. Take something like labels. They apply at the repo level and not the project level, so when you add issues from multiple repos, managing labels becomes an administrative task.

View creation is confusing and painful, due to the flexibility (which used to be a common complaint about Jira until they removed the many hundreds of options). People struggle to understand what comma does in the label list vs a space with a new label key/value.

Workflows are also per project and have to be replicated for every project and there's no global default template you can define.

Dependencies are non existent, so order of operations can't be defined in a way that's meaningful. You can order tasks but not indicate "dependency a is not complete and you may move on" in a simple way.

Task lists can't be reordered without editing the markup, which is finicky. If there's a newline it doesn't like, it errors. If there's a character wrong, it errors. Sometimes it just errors and you have to delete the whole thing and recreate it from scratch for it to render again.

There's no "move to top" or "move to bottom," which is necessary when you have long lista of items.

It's improving and if everything is a code, it's probably fine but when you're doing projects, some things are just tasks and it's not well suited for that, in my opinion.

I'm sure it will improve (as of last week you can limit WIP and export views as a CSV) but it feels so much like it's catching up, slowly, that I don't see it ever becoming a "good" alternative to systems that already exist.

I could list more but I'd have to look at my computer and there is already enough here that I'm just pulling from memory.

Not OP but also using GitHub Projects. Up until recently projects was just missing critical features like true epics and first class parent child relationships between issues. These are slowly getting added though. There is an entire product called Zenhub that exists to make GitHub issue tracking more sane. I will say the automation story in GitHub Projects is better than Jira imo