That's an interesting point, and indeed NT has a curious history in that regard - Microsoft was originally planning an OS/2-based API as the dominant one, and it was only due to the success of Windows 3.0 that they ended up adapting the Windows API to 32 bits.

Microsoft has always been dominated by backwards compatibility constraints so there probably wasn't much scope for a massive redesign of the API, as it was in their best commercial interests for 16 and 32 bit Windows APIs to match as closely as possible, to ease porting of third party software.