Second, we've got the Civs themselves. This is entirely predictable - beginning with Civ 3, Civs have been growing more and more diverse - and that means less and less balanced. However, I would say that Civ V is the first game where there is a definite tier system in play, and I would argue that this is because in Civ V, the Civ distinctives actively shape the way the Civ plays. This can be a good thing or a bad thing, depending on your point of view. In Civ IV, most of the traits were transferable to a variety of victory conditions and playstyles. In Civ V, while the best Civs tend to have abilities that are transferable, most do not.
This is good in the sense that there is a lot more variety between the Civs, and playing one Civ will feel fairly different from playing another (though there is not quite so much variety as there is in a game like SMAC). However, it's bad in the sense that the power divide between different Civs is far larger than ever before, and there's a distressing amount of Civs who require specific map conditions, setups, and/or gameplay styles to be competitive - made even worse by the fact that there's quite a few Civs who are incredibly powerful in virtually any situation.
Personally, I prefer Civ IV's Civs. While I like the variety of Civ V, I feel that too many Civs are pigeonholed into either specific playstyles or specific map requirements. In Civ IV, the Japanese were arguably the worst Civ, but they weren't at too large of a disadvantage (and most of the disadvantage they did have wasn't from the Civ itself, but rather from their idiot personality's isolationist policies). In Civ V, the Danes are arguably the worst Civ, and holy crap, do they struggle.
For me, I see Civ V's Unique Abilities the same way I see a lot of changes the game made: Good idea, bad execution.