Microsoft learned from the mistakes IBM forced on them and did a better job. Right off the top of my head:
* IBM forced 80286 compatibility in an 80386 world.
* IBM forced incompatibility between Windows and OS/2 for the sake of preserving their mainframe graphics API's.
* OS/2 had a single messaging queue for the whole desktop.
* OS/2 was tied to the underlying hardware to the extent of being written partly in assembler.
OS/2 was great... I loved OS/2 2.0 in particular (and I worked for IBM testing OS/2 LAN Server for a summer)... but IBM had no idea how to address the market and no sense of how fast it was evolving.
In a more Microsoft-centric world, I'm pretty sure the OS/2 API would've been exactly as you describe it and almost strictly in parallel with Windows. In fact, Microsoft did exactly this with Win32s (and Windows 95) In their relationship with Windows NT (which was once known as OS/2 NT or OS/2 3.0).
The same compiled binary could run on both the 'entry level' OS and the 'server level' OS, with a bit of care taken in the way the API was used.
That's a fairly broad description, isn't it? At least I have a hard time coming up with windowing API models that don't fundamentally work that way at the lower levels. (About the only exception think of is a text-based library that shipped with Microsoft BASIC 7.0, and that was mainly because the language didn't support any of the abstractions needed for callbacks.)
However OS/2 had many other layers to it's programming SDK that were not found in early Windows.
For example there was the Dos layer for things like processes, threads, semaphores, files, directories etc.
And then there was the Gdi layer for graphics.
Most of that functionality only made it's way into Windows with the advent of Windows NT (Windows 3.x/95 had poorer versions of those functions. For example running a process and capturing it's output was a real pain in Windows 3.x and Windows 95).
And based on the fact so many of those OS/2 Dos function have an equivalent Windows NT version I suspect Microsoft used that OS/2 design as their starting point for NT.
As just one of many examples consider DosCreateThread from OS/2 1.x
http://www.edm2.com/index.php/DosCreateThread_(OS/2_1.x)
It looks a lot like the CreateThread function found in Win32:
https://docs.microsoft.com/en-us/windows/win32/api/processth...
So the question is, back then was there any better GUI programming layers?
And the answer is yes, there was actually an API that was better and it was called OS/2.
At that time Microsoft was in a partnership with IBM to develop OS/2.
However, when the partnership fell apart, Microsoft just took big chunks of that OS/2 API and created a sub par version and called it the Windows API.