The width and height given to the Phaser.Game constructor can now be numbers or strings in which case the value is treated as a percentage. For example a value of "100%" for the width and height will tell Phaser to size the game to match the parent container dimensions exactly (or the browser window if no parent is given). Equally a size of "50%" would tell it to be half the size of the parent. The values are retained even through resize events, allowing it to maintain a percentage size based on the parent even as it updates.
Stage.offset has been moved to ScaleManager.offset
Stage.bounds has been removed, you can access it via Stage.getBounds.
Stage.checkOffsetInterval has been moved to ScaleManager.trackParentInterval
ScaleManager.hasResized signal has been removed. Use ScaleManager.setResizeCallback instead.
Moved the DOM offset from Stage to ScaleManager (a more logical location for it) and updated Pointer to use that.
Moved the Pointer offset check to look at the ScaleManager.
Used getBoundingClientRect(), will see if that works better than Phaser.Canvas.getOffset.
Input.Gamepad.destroy now destroys all connected SinglePads and clears event listeners.
SinglePad.destroy now clears all associated GamepadButton objects and signals.
Pointer.withinGame is now accurate based on game scale and updated as the Pointer moves.
Stage.bounds is now updated if the game canvas offset changes position. Note that it gives the un-scaled game dimensions.
P2.Body.applyForce should have used pxmi instead of pxm (thanks @Trufi, fix#776)
P2 fixed creation of RevoluteConstraint by passing maxForce in the options (thanks @woutercommandeur, fix#783)
If the game was set to NO_SCALE and you swapped orientation, it would pause and resize, then fail to resize when you swapped back (thanks starnut, fixes#258)
If your game references the old Phaser.StageScaleMode consts like SHOW_ALL you need to update them to Phaser.ScaleManager, i.e. Phaser.ScaleManager.SHOW_ALL.
All of the Project Templates have been updated to reflect the above change.