The way a browser works is that it's a renderer with a "frame" overtop of it. The IE renderer is called Trident, the Chrome and Safari renderers are called "Webkit" and the Firefox renderer is called "Gecko".
Making a renderer is not easy, especially not directly from scratch to compete with other renderers. What Microsoft will probably do is a discrete rebrand, where they change the GUI/frontend of IE and simply update the shit out of Trident. So, it'll really just be IE 12 with a new skin. That means that all applications designed only for IE (old Silverlight apps, etc.) will still work with Spartan.
That's just my speculation though.