A few things I know of,
Ships now have new anniversary skins, and when they die fireworks explode out of them
Some new shop items
Some major changes on the Spire also,
Med guns on the sides rotated more forward, making it possible to fire all four guns forward
Hull moved to mid deck by the main engine
Balloon moved to bottom deck
Hull reduced to 400
And then Resource Race was removed from the game, replaced by Crazy King.
There is most likely a lot more, but this is all I personally know about. If anyone is aware of anymore changes they should I guess post them as well.