Yes, the hard part is replacing cmd.exe (i.e. making a terminal that works with windows programs). Making a terminal that works only with linux programs should be fairly simple, especially with WSL (windows linux subsystem)
Actually cmd.exe isn't the problem. conhost.exe is. Whatever you run on windows CLI, be it CMD, Powershell or BASH, it runs on conhost.exe. Even ConEmu and Console2 are just wrappers around it. The console host is getting better though. The latest W10 release supports arbitrary resizing of the screen atleast :)
In the next update we even get 24-bit color.