Well, for starters, WinUI 3 is Windows only (correct me if I’m wrong), while Avalonia supports Windows, MacOS, Linux, Android, iOS and WebAssembly.
The cross-platform solution that Microsoft advocates for is MAUI, which doesn’t support Linux. And it uses native controls, meaning you may encounter platform-specific bugs, while Avalonia renders the controls the same way everywhere using Skia (same approach with Flutter).
Oh boy, now I need to find a new excuse to procrastinate on the project I want to start using Avalonia.