Why is it so difficult to run Windows software natively on another operating system?

Windows programs are built against Windows-specific APIs, system behavior, libraries, and sometimes drivers. To run them natively, another operating system would need to reproduce all of those interfaces and the subtle behavior applications expect. That is a huge amount of work, especially because some behavior is undocumented or changes between Windows versions.

Projects like ReactOS are attempting essentially this: they reimplement the Windows operating-system interfaces rather than just translating individual programs. The problem is that an operating system is extremely complex, and compatibility requires supporting far more than basic file access and windows. Applications may depend on graphics systems, copy protection, installers, codecs, unusual bugs, or proprietary drivers, so partial compatibility is common.

Wine and Proton already make a large number of Windows applications and games work, but they are compatibility layers, not complete replacements for Windows. Their success varies by program. Games have improved considerably because of work around graphics APIs and gaming tools, while applications such as some versions of Microsoft Office may rely on Windows components that are especially difficult to reproduce. The software being closed-source makes understanding its internals harder, but the biggest issue is the enormous engineering effort required.