There is no perfect issue tracking system sadly and integration with prs and commits actually is becoming a hard requirement for me. This is not something that people should be updating to an issue tracker manually, ever. Or doing without entirely (more common). Also nice in Github is the integration with Github actions and being able to see whether something can be merged safely or not.
I double as a product manager and CTO, meaning I do both code and planning. We're using Github issues and Asana. Both have their strengths and weaknesses. I'd take both over Jira any day. And since I'm in charge, my company is blissfully free of anything Atlassian.
I kind of like Asana for planning. It's got a few sane features one of which is separating issues from projects. This allows me to quickly plan out projects and then add tickets to the relevant team boards. And another one is making it very easy to create issues in a spreadsheet like view that minimizes the click bureaucracy other tools have. Great when you basically are thinking at the bullet point level and just want to hit enter instead of having to fiddle with obnoxious modal forms.
Of course for developers Asana isn't great because it has no markdown support and no usable github integration (a few commercial things exist but they are basically glorified sync tools). Github issues have a few nice features as well. I like working with check lists and then converting the individual items to tasks. That comes close to how I like to use Asana.
Where Github falls off a cliff is what passes for project management. I don't know what their PMs were smoking but it's just completely wrong and useless. It kind of lives orthogonal to issues (!!!!!) and nothing syncs automatically except with really awkward github actions crap. So, it only serves to add a lot of bureaucracy and busy work without actually addressing the core problem. A combination of over engineered and inadequate.
The core issue with Github is that issues are tied to a single code repository. From a planning point of view that is just horrible because I manage a product consisting of multiple code repositories and I need one plan that may involve zero or more code repositories and not several and I don't want to lock in my issues to a single repository before I have even figured out what the plan is. I guess that's what they tried to fix with their project management thingy. Except they messed that up badly.
I'd love a tool that is a bit like Asana but more integrated with pull requests, CI/CD, the notion of work being distributed across multiple code repositories, teams, etc. I don't mean yet another sync thingy that copies tickets from system X to system Y. I would like a one stop shop that can be used throughout the life cycle of a software product from before any code is written until users / customers start reporting issues and everything in between. Doesn't exist.