In the past 12 months, I've had an M7, Moto X, Note 3, G2, and now a Nexus 5. The only one I would hands down say I like the Nexus 5 better than is the Note 3. TouchWiz sucks. The others all had high points that they beat the Nexus on and weaknesses where they lose to the Nexus (with the possible exception of the G2, but we'll get to that).
The M7 had a camera that worked really well for me. I know it wasn't the best camera, but it was one of the best for how I personally use a phone camera, only being surpassed by the G2. The M7 also feels great in the hand, I love the metal construction. The M7 was nice because I unlocked the bootloader and was S-Off which enabled me to go back an forth between Sense and GPe (OTA's and everything in both setups). Front speakers are also a big plus IMO. However, the Nexus has a bigger screen in a smaller form factor and faster updates. The camera on the Nexus also seems to be pretty good so far. Overall, I do not think one is clearly better than the other, but I think I prefer the N5.
The Moto X Active Display, Touchless Control, and Moto Maker customization are all high points where the Nexus loses. It was also more one hand friendly than the Nexus. However, I like the extra screen realestate I get on the N5. Again there is the updates issue. The Moto X got 4.4 very quickly, but it took a very, very long time to get 4.4.2, and 4.4.2 addressed some bugs that were extremely inconvenient to live with. Then there is the camera. The Moto X's camera is garbage. It was simply too bad to live with. If the Moto X had a camera on par with the N5, I'd still use a Moto X. The camera on the X is so bad, that it completely erases any advantages it has over the N5 (or G2), and for that reason I prefer the N5 to the Moto X.
Now for the Note 3. Great hardware. Feels great in the hand, I love the big screen, and I love the S-Pen. The camera, while not on the same level as the G2, is very good. However, TouchWiz is terrible. It completely ruins the phone. If the Note 3 ran stock Android, Moto's build of Android, or LG's build of Android, I'd love it. However, it doesn't, and because of how terrible TouchWiz is, I prefer the Nexus 5.
Finally, my most recent pre-Nexus phone, the Nexus 5's sister device, the LG G2. What can I say about the G2? It is almost the same size as the Nexus 5, but you get .2" more screen. The camera kills the Nexus 5's camera, and just about any other phone camera out there. The battery life on the G2 is phenomenal. Once I installed Nova Prime (which I use on every phone), there was not one thing about the LG UI I had a problem with, and there were a few things I genuinely enjoyed. The back buttons and Knock On are amazing and I miss them badly. Q-Slide (their multi app setup) is fantastic. Sure, the G2 won't get updates as quickly as the Nexus 5, but that is about the only thing that I consider a legitimate advantage of the N5 over the G2. I gave my G2 to my mother-in-law cause I thought she'd like it better than a Nexus 5. I think the G2 is a great phone, and I like it better than I like my Nexus 5. Even knowing the G3 is coming out soon, the G2 is being sold at a price that I would not hesitate to buy it today. I got my wife one recently, got my mother-in-law one, and tried to get my brother-in-law to get one instead of an S5.
TL/DR: I've had a lot of phones this year. The N5 is as good as or better than all of them except the G2. The G2 rocks.