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.
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.
https://frippery.org/busybox/index.html
It has a subset of bash implemented on Ash/Dash. Arrays are not supported, but it is quite fast.
The forking problem is still present, though.
For example, someone might do something like this (completely ignoring the need to quote in the interests of illustrating the actual issue, forking):
for x in *; do
new_name=$(echo $x | sed 's/old/new/')
mv $x $new_name
done
for x in *; do
echo $x
done | sed -r 's|(.*)old(.*)|mv \1old\2 \1new\2|' | grep '^mv ' | bash
Of course the code as written is completely unusuable in the presence of spaces or other weird characters in filenames, do not use this.
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.
Java was ahead of its time, now nothing has a coherent UI toolkit.
Cygwin doesn't work at all in Windows AppContainer package isolation; too many voodoo hacks. MSYS2 uses it to this day, and as a result you can't run any MSYS2 binaries in an AppContainer. Had to take a completely different route for Claude Code sandboxing because of this: Claude Code wants Git for Windows, and Git for Windows distributes MSYS2-built binaries of bash.exe and friends. Truly native Windows builds don't do all the unusual compatibility hacks that cygwin1.dll requires; I found non-MSYS2-built binaries of the same programs all ran fine in AppContainer.
I was a Cygwin user from about 1999 to 2022 or so, spent a little time on wsl2 (and it's what I still use on my laptop) but I'm fully Linux on the desktop since last year.
Interix was implemented as proper NT kernel "subsystem". It was just another build target for GNU automake, for example.
(Being that Interix was a real kernel subsystem I have this fever dream idea of a text-mode "distribution" of NT running w/o any Win32 subsystem.)
Requiring every single Linux app developer to recompile their app using Cygwin and account for quirks that it may have is not the correct approach. Having Microsoft handle all of the compatibility concerns scales much better.