Based on my experience I definitely think they are.
Prior to my Nexus 5 the only Android experience I had was a few minutes here and there with a friend's older HTC, a friend's Galaxy S3 and probably an hour or so playing with the Galaxy S4 and S5 in Best Buy. Before the Nexus my only smart phones had been the iPhone, of which I've owned every generation.
Based on my pre-Nexus experience I thought the Android OS' was very clunky unintuitive. Every action seemed to have a bit of lag to it, the experience in one app was different from another app, there was no uniformity, etc. But, from what I understood, you could change everything. Not the best option for probably 80-90% of consumers, but it's an option.
Anyway, after seeing flame war after flame war from both sides for years I found myself in a situation where I could pick up an Android phone to use until the iPhone 6 comes out, at which time I may (which has been my plan) or may not upgrade. After doing lots of reading and talking with friends I chose the Nexus 5. It's specs were nice and whatnot but I was sold on the fact that it's as close to Apple and the iPhone as one could really expect from the Android world, it's Google's baby with the most vanilla Android version.
My experience with it has been much different and much better than what I had experience before. Little to no lag is apparent outside of the camera app, a lot more behaviors are found across multiple applications, layout within stock apps is more uniform, etc. It feels a bit more intuitive, which was the biggest hurdle. Going back and playing with a Galaxy S5 after owning my Nexus I still feel like the Galaxy has a clunky & unintuitive feel. That alone has cemented the idea that OP was getting at. Now that I've got a good feel for the OS I can't blame the odd feeling from other phones/skins on my ignorance of the OS in general, I can instead blame it on poor design from the individual manufacturers.
With that said, at this point I'm still planning on upgrading to the iPhone 6 when it's released. I enjoy my Nexus but every few days I find another missing feature (compared to iOS), or significantly changed feature thanks to a software update, etc. Within a day or so of purchase the camera app looked entirely different than it did when I first launched it. Just a week or two ago I noticed I was mistyping a lot of characters, thanks to a keyboard updating rolling out. Etc. I realize that many consider this a development platform for Google, but it still seems crazy to me that as a new user I can't rely on the core apps/functions remaining static or seeing slow changes rather than these major changes. I mean really, the keyboard layout was altered. I can't think of any good reasons for this.