The Moto X has hands-free voice control, which is pretty cool. I already enjoy saying "Okay, Google" on my N5, and doing that on the Moto X without having to turn it on and swipe it open would be even cooler.
The N5 may have the more powerful SD800, but it has twice the number of pixels to push, so it doesn't feel any faster. I don't know what the battery life is on the Moto X, but I imagine it would be better, because once again it has half the number of pixels to light up. In fact I wouldn't be surprised if the battery life was significantly longer during on-screen testing.
The Moto X also feels better in the hand, which is really important. I bought a white N5 and it's incredibly slippery, no grip at all, I've already dropped it twice and one time it slipped and flew out of my hand when I pulled it out of my pocket in a hurry. My leather case that I ordered for it can't get here fast enough. I bought the Nexus 5 before all the reviews came out. If I had known the white version had no grip and was slick as ice, I would have bought the black version instead. The white N5 feels like you're holding onto a wet bar of soap, it's that slippery.
The speaker absolutely sucks on the Nexus 5. That alone almost killed it for me the first time I watched a video and found out I have to hold my thumb in an awkward position to prevent my thumb from blocking the speaker.
The N5 may have the larger screen, but it's difficult to operate with one hand. The Moto X fits perfectly in your hand though and you can use it one handed comfortably and easily.
Honestly if I had known the Moto X was going to drop to $349 off-contract, I would have bought that instead. But oh well. The Nexus 5 is still a beast of a phone and I like it very much, despite all of its flaws.