I use Mintty because Cygwin's tmux didn't work with ConEmu or Cmder, but Mintty was ok.
FWIW, I took a quick stab at the tmux & ncurses code to try to find a fix, but it was far from obvious. Maximus (ConEmu author) said it had to do with how cygwin flags stdin streams, which just happens to break when ConEmu provides them. (sorry details vague)
Quickly scanning the code, it looks like ConEmu is using hooking to implement the Win32 console API and forward calls to the terminal emulator. That's a good approach, but it needs to be integrated into the Cygwin pty system to really work well in that environment.
The problem I have with console replacements is most of them break readline. You can't run many interactive programs with them. On the other hand, you can't have full unicode support without a console replacement.
Indeed. People need to stop thinking in terms of building win32 "terminal emulators" (most of which involve god-awful hacks, like scraping hidden conhost windows) and instead emulate the Win32 console API in userspace (just like Windows itself did before Windows 7) and implement the Cygwin pty interface in terms of this library. This way, Cygwin programs think they have a pty and Win32 programs think they have a console, and everything Just Works.
But people would rather just hack up a "terminal emulator" instead of doing things the properly and the hard way.
No, give cmder a shot: http://bliker.github.io/cmder/ I've tried mintty and cmder, and cmder was just perfect for me.