The big flaws in Civ 5 lie in the AI and the execution of the features, for example:

Hexes are great, except the AI cannot handle them.
Moving units over sea without transports is great, except the AI doesn't understand the difference and treats it as land. Running units into your navies to be destroyed at will.
Diplomacy is gimped, if you have a border with any Civ they WILL declare war on you.

Etc.