There are several new abilities and game mechanics introduced in
The Eye of Judgment: Biolith Rebellion 2 (Set 2). New abilities include: Decoy, Fieldmorph (to the field type of the creature), Intercept, Invocation, Magic Protection, Resurrection and Return. (If a character has Resurrection and you have another in your hand, you can instantly replace the fallen one with the one from your hand; Return merely means that you return a fallen character to your hand.)
New game mechanics that shake things up a bit include: new creatures that cannot be attacked with Spells, new creatures that prohibit certain abilities (such as the way that enemies within two squares in front of a Dwarf Sniper cannot Dodge.), the ability to steal exit mana from destroyed creatures, the ability to create combination Fields, the ability to get cards from your deck library or graveyard, spells that deal direct damage to creatures and spells that influence turns (such as Aluhjan Spellsheild).
The above mentioned updates include some upgrades that are, technically, not part of The Eye of Judgment: Biolith Rebellion 2 (Set 2), such as improved graphic displays showing more information about Field and Card Status and a new in-game encyclopedia explaining everything you could need to know, regardless of skill level.
And, don't worry if your friend hasn't upgraded, yet... players who have Set 2 will still be able to play against players who only have Set 1.