Windows 3.x was way more successful than Microsoft anticipated. They wanted to pivot the Win32 layer in NT to be the primary API and make the user interface more Windows-like. IBM didn't want that so they parted ways.
David Cutler (designer of VMS) was the architect for NT. Many people don't know it has a single root filesystem that takes the unix philosophy even further... objects like mutexes exist in the root, not just files. Everything has full ACL support. The IO completion ports and async support were way ahead of their time. It originally even ran things like the video driver in user space.
Windows 3.x being so successful almost killed everything that was great about NT. It also caused Microsoft to completely miss the mobile revolution.
Success hides problems indeed.