Quoted from the front page of the official GaK website:
"World Domination
The fight for world domination is now more dynamic than ever before. The Gods and Kings expansion features a reworked combat system and AI that puts more emphasis on a balanced army composition. The new system allows your lines to stand longer than they could before, so you, as a player, can make smarter tactical decisions without worrying about a single unlucky roll of the dice."
"Naval Combat
Your navy is now split into two different ship types, melee and ranged. This means that no coastal city should be considered safe, and can now fall to a surprise naval attack. Additionally, all embarked units now have Defensive Embarkation, and can stack with a naval unit for extra protection. Add to this the new Great Admiral, and the high seas have become a much more dangerous place."
So, embarked units that can defend and stack with a ship (but if the protector ship sinks, what happens to the unit under it?) and improved AI army composition. It doesn't promise the AI can organize the better army into something useful, however.