I am still waiting for the delivery of my Master Edition (collectors) of Index Card RPG Master Edition, but I found this great post on the differences between 2e (which I have and likely many others since it is still up on Amazon), and the newer addition, check it out:
There seems to be an item missing from the above list, equipment tags have been removed from the game. I suppose it is easy enough to say, "you are using a long weapon in an airshaft, the roll is hard" without a tag needing to guide you. I did like the tag system, but I can see how it was very subjective, may or may not apply in different situations, and makes you feel your rulings should be forced in some situations when ultimately it is up to the referee to decide.
Many of the "in play" rules are the same, and many around character creation and progression have been streamlined and better and more consistent options given no matter the genre.
I wish the book would come so I can give it a look over, as I am not a huge fan of playing from PDFs. I could print a copy of the core rules and player's section out, but the book should be close to shipping so I don't feel like printing 70 pages for little use.
The new edition looks like a fun, streamlined, and internally consistent version and I am looking forward to giving it a look.