I think this thread has a good discussion on the merits and demerits of Civilization 5.
Quite a few pros and cons are discussed. Perhaps it could be of some use.
http://forums.civfanatics.com/showthread.php?t=394565&highlight=crispy+gamer
As far as Religion goes, it added depth and made diplomacy interesting.
It also modeled world history fairly well. Many wars have been started in the name of religion down through the ages. After the scientific revolution, the reason for wars became more because of nationalism than religion. It also added depth and personality to the AI Civs which are now just hollow drones and as interesting as a stack of wet newspapers.
Trade routes are also a total joke. Not realistic and simplified to the point that everything merely trades through your capital. It's not complex, interesting or realistic.
Also, when you trade resources with an AI Civ, you don't even need to trace a trade route with him/her. The resource magically teleports to you. It even teleports from the trading partner over enemy territory, even if you are at war with that enemy.
This game was obviously released far too early. At least one year too early if not two.
The truly sad thing is that the only area that might even be considered more complex (and that is debatable) is the combat system. However, the AI is so awful that any complexity to do with the combat system is quickly forgotten as the AI is too moronic to use it even remotely correctly. At least in cIV, the AI could use the stack system fairly effectively and present a reasonable challenge.
That likely won't change in the future. As Jon Shafer himself said, it isn't worth it financially to build a great AI. For that reason alone, the game is and will remain quite mediocre. Adding more complexity will not be deemed financially viable for that reason. The future is bleak.