Mage Knight had several rules releases in its original run, and the core HeroClix rules have evolved significantly as well since that time. The cool thing about this Kickstarter is that it allows us to interact directly with fans to figure out what worked and what shouldn't be imported into the new set.
So, while we'll go into this more in a later update, the answer is that MKR will run on a core of modern HeroClix rules but with an extensive array of modifications to include all the favorite elements from various Mage Knight releases. Since this rules set will be internal to the video game, you don't need to worry about backwards compatibility.
The physical bonus figures will have swappable dials. One dial will use modern HeroClix core rules. The other will be compatible with Mage Knight 1.0 figures.