Cygwin is way older than CoLinux. CoLinux is from 2004. Cygwin was first released in 1995.
The problem with Cygwin as I remember it was DLL hell. You'd have applications (such as a OpenSSH port for Windows) which would include their own cygwin1.dll and then you'd have issues with different versions of said DLL.
Cygwin had less overhead which mattered in a world of limited RAM and heavy, limited swapping (x86-32, limited I/O, PATA, ...).
Those constraints also meant native applications instead of Web 2.0 NodeJS and what not. Java specifically had a bad name, and back then not even a coherent UI toolkit.
As always: two steps forward, one step back.
Just use ssh from Cygwin. DLL hell was rarely a problem, just always install everything via setup.exe.
The single biggest problem it has is slow forking. I learned to write my scripts in pure bash as much as possible, or as a composition of streaming executables, and avoid executing an executable per line of input or similar.
Meanwhile those that complained about Java, now ship a whole browser with their "native" application, and then complain about Google taking over the Web.
> Cygwin had less overhead which mattered in a world of limited RAM and heavy, limited swapping (x86-32, limited I/O, PATA, ...).
Maybe so, but my memory of Cygwin was waiting multiple seconds just for the Cygwin CLI prompt to load. It was very slow on my machines.