The OS/2 subsystem only ever emulated OS/2 1.x, it never emulated OS/2 2.x or later. That severely limited its usefulness. Also, it only supported text mode apps out of the box, and the GUI was only available from Microsoft as an add-on sold separately (which very few people bought)
There was never a huge amount of OS/2 software anyway. And a lot of what software was available for OS/2, also had native Windows versions, so why bother emulating the OS/2 version when you can just switch to the native app?
A lot of people ran OS/2 1.x because it was the basis of Microsoft's networking solution, Microsoft LAN Manager – which as well as being sold by Microsoft, was also sold in OEM versions from IBM, HP, 3Com, among others. But rather than trying to run OS/2-based LAN Manager under NT, people used NT's native implementation of the LAN Manager protocols (SMB File & Print)
I think the POSIX subsystem could have been a lot more successful if Microsoft had invested in it more. But I think Microsoft was worried about investing in it too much, because if UNIX software can run on Windows, a lot of developers might just write UNIX software only, not write to the native Win32 API, and then there would be less switching costs to move that software off Windows and on to UNIX or Linux.
What is different about WSL, is that by now POSIX has clearly won the battle for developer mindshare, and Microsoft has decided their best interests are to cooperate with it fully rather than continue in their prior hesitancy about it. But they've had 20+ years to watch it win in the market, and that's informed their change of heart.