PuTTy is already an incompatible mess all of it's own. It even has it's own special format for keys, so we get the joy of running every ssh key generated on a *nix system through puttygen.exe just to spit out some fugly PPK file. Oh, you need me to add your public key to authorized_keys? What's that you say? You used puttygen? Well fuck me, time to look up the command to convert that stupid shit again. Wonderful!
Not to mention the fractured disorganization of the configuration, the crap profile system and all the other reasons why PuTTy is a pain in the ass.
The fact that Microsoft is talking about using OpenSSH means at the very least the key files will be compatible. I have no idea why no one bothered porting OpenSSH to Windows before, but it's about damn time! I'm looking forward to a version of PuTTy (or KiTTy, actually) that uses the native OpenSSH instead of the existing legacy PuTTy implementation of SSH. I'd love to delete all those PPK files and never see another one again as long as I live.