Welcome to Android Central! I look at it in a somewhat different way. It's true that "stock" Android on Nexus devices don't have a lot of the extra added features you might find on Samsung or HTC phones, but I don't see this as a disadvantage. The problem with having extra features added by the manufacturer is that they typically can't be removed--you're stuck with them, even if you never use them. This can be a bother if you start running low on storage, since those extra apps/features do take up space. With Nexus devices, you just pick and choose what kinds of added features you want by choosing them from the Google Play Store. (This doesn't mean, though, that you can duplicate every kind of manufacturer-installed feature by using an app on the Play Store.)
Prompt system updates directly from Google are another big advantage of Nexus devices. There's no need for the updates to go through the manufacturer and the carrier to be tweaked. Google's monthly security patches also come through without significant delay, which may be important to you if security is one of your top priorities.
The fact that there is no additional overlay from the manufacturer or carrier also means that there is much less chance that the updates will cause any glitches. When updates go to non-Nexus devices, the code has to be tweaked by the manufacturer and the carrier to work correctly with all of the various modifications and features they added to the base Android code. That's usually what leads to glitchy updates.