The problem with (1) is it's inherent to the design concept. Nix defines package identity to include the dependency closure. Fixing that would require introducing the concept of an interface export that blocks the recursion, and then having other packages depend on that. This is nothing radical and plenty of build tools do it e.g. Gradle has a concept of this, as does a private build system I built myself. But Nix doesn't have it, it's something that would have needed to be there from day one, and AFAIK there are no plans to add it. Also by the time you're done with this it doesn't look much different to a conventional package manager.

Incompatibilities can of course happen, but so can improvements. Nix throws the baby out with the bathwater. You can rerun CI of upstream (open source) projects against a new set of component versions if you want, it doesn't imply anything about how the distribution mechanism should work.

For (2) the issue is non-downgradeable data, not non-upgradeable. Apps basically never support downgrades. Consider your web browser changing the format of its HTTP cache or credentials store, consider your word processor adding a new feature that the user incorporates into their documents and then it's suddenly downgraded. There isn't even any way to downgrade Chrome via its normal user interfaces!

For (3) crashes aren't just annoying, they're indicative of a fatal design flaw. Native plugins were a common feature on other operating systems in the past and have historically been a feature of KDE and GNOME too. I don't know if there are new Linux-native apps of high complexity being written these days though. The dominance of Electron means plugins have moved server-side where the user's OS can't screw them up. Nonetheless, you can't have a serious productivity-focused desktop OS if apps can't be composed at all. You can at best maybe do a ChromeOS competitor.

For (4) sure it can be just defined as out of scope, same thing Nix[OS] does with lots of other important problems. It's embarrassing to present Linux as a solution if it depends on Microsoft to solve the hard stuff for you, though.