First, let me preface this with the fact that, in my opinion, overall it's a pretty solid OS. After having done research several times, the only other mod I've considered is LineageOS, but last I checked, there were no builds for my Pixel 6 Pro.
My biggest two issues with it are that it doesn't have any usability improvements other mods have. It's not on them though, as it's an expectation I have of mods, but obviously this is like having an expectation of support for FLOSS. It's annoying, but it is what it is.
The default camera app is subpar compared to the stock camera app of Pixel phones. I use OpenCamera, but it's also not great (though that opinion might stem from me not knowing how to use it properly).
The bigger issue I have with it is that, while sandboxed Google services generally work pretty well, some apps don't work properly with the location requests proxy. I'd love to enable it, but, for example, Citymapper is unable to track me when I use it. Finding a location sometimes can take very long.
I would love to have LineageOS improved by having the hardening patches that are in GrapheneOS.