Honestly, fir me, it's not a specific thing, so much as a characteristic. It's the fact that they come up with great ideas and then manage to screw them over in execution. The game is great and so are most of the aspects, but they manage to shoot themselves in the foot by doing it in such a way that it really makes you scratch your head.
Let's take the Leader Selector as an example.
It's a great idea. One that I'd been wanting for ages. Common sense approach would be to have a drop down menu next to each random civ that allows you to just deselect whichever civ you don't want in that slot. Possibly have preselected groups, but it would be easy and simple.
Instead, they do it so that you have two leader pools from which you can select or remove leaders and you have to have at least as many leaders in the pool as you do players in the game. So, if you want certain leaders for definite then a choice between certain leaders for one random, it becomes a right hassle, and you can't do that and have duplicates as well. I can't figure out why they did it that way.
There a lots of great ideas in the game and it is a great game, but it's frustrating to see that potential and have them fall short because of bizarre choices that make no sense.