I hate the fact that embarked units can be destroyed in one hit in vanilla, and you can't even stack naval units on top of them. Is there a mod to fix it? Is it the same in Gods and Kings?
To defend embarked units in vanilla:
- Remember that they don't die in one hit in general, they just can be destroyed by naval units that "walk" into them. In other words, ranged attacks do not always insta-kill them.
- Remember that moving from a hex adjacent to one of your ship to another hex adjacent to one of your ships will deplete the entire turn for the enemy ship - in other words, if you keep your navy in front with gaps of two hexes or less, you can effectively block enemy ships from moving into your embarked units.
- If you get really frustrated, play as Songhai - their embarked units can defend themselves, so naval units can no longer "just move" into them - though they still suffer heavy damage.
Things are very different in G&K:
- All embarked units can defend themselves, same way the Songhai units can in vanilla.
- You can stack naval units on top of embarked units, defending them.
- You can use melee naval units to conquer cities, so you don't have to deploy melee ground units for that.
In general, the naval combat in G&K is significantly revised, especially with the separation of naval units into melee and ranged units.
I don't know about mods, but in G&K embarked units are supposed to have some defense. Obviously not high defense if it gets killed by Caravel.
You didn't mention what civ you were playing, but in this situation Songhai is perfect. Songhai gets extra defense for embarked units in G&K (in vanilla, they were the only civ with embarked defense so had to give them something more in G&K) and Songhai units all spawn with amphibious, so they can mount naval invasion without fear.