Have you considered making it a Unity 3D Tool?
Viewing post in Multi-tile Selection is Here! comments
I have the skillset to make this a Unity tool, but I'd need a compelling reason to. Blender gives users the most flexibility with their workflows, being a dedicated 3D software. For now you can easily get take the models you create in Blender + Sprytile and import them into Unity. If you're not familiar with Blender, there is some work required learn the software, but I think it's a worthwhile investment for what you get out of Blender.