HTC Nexus One
Google's first foray with their own phone was a spectacular thing. It offered hardware no other Android phone manufacturers were doing. A gigahertz Snapdragon processor, 3.7" display large for it's time), 800x480 resolution (high resolution for it's time), and excellent material choice (thanks, HTC!). However, their next two Nexuses (Nexi?) weren't ground breaking. They just tacked on a few experimental features.
Specs and feature-wise, it didn't feel like it was missing anything. Of course, it did have a problem with multi-touch, which was never fixed because it was a hardware limitation. Here are some sites that reported on this. You can also search for videos demonstrating this problem on YouTube. Oh, and lets not forget issue with the constant switching between Edge and 3G reported at places like here and followed up at places like here. Spoiler alert: Google just gave up.
Samsung Nexus S
The Nexus S was a single core Hummingbird SoC, which is fast, but it came at a time where dual-core SoCs already exists. They took away expandable storage. The other stuff (Super AMOLED display, 5 MP camera) were considered standard fare, since the Galaxy S was already on the market.
Of course, Google added NFC, which is the experimental sauce I was talking about earlier. The curved glass was more of a gimmick, though. It's a nice touch, but it doesn't really add any new functions.
Samsung Galaxy Nexus
Next was the Galaxy Nexus. First off, the name is dumb. Because Samsung already has a line of Galaxy phones, this just causes confusion. Every time I hear "Galaxy Nexus", I keep thinking "Galaxy S" or "Galaxy S II". Every time I want to say "Galaxy Nexus" I end up saying "Galaxy S" which confuses people and myself.
Name aside, it also wasn't very ground breaking compared to other phones in the market (especially when compared to the Galaxy S II). It's got a better screen (720p 16:9 display), even though it's a PenTile matrix. They also did away with buttons on the front, instead putting them on the screen itself. Other than that, nothing else is really new to us. And yes, NFC decided to stick around on the Nexus Galaxy.
It's now a dual-core SoC, but quad-cores are coming now (they should have waited to add this in, honestly). The camera is still 5MP, but what's worse is that it's not as good as the 5MP sensor Apple used on their iPhone 4. To add insult to injury, Samsung already has an excellent 8MP sensor that's used by their 2nd gen Galaxy phones (Galaxy S II, Inspire, Galaxy Note, etc). Of course it can capture 1080p video now - that's just a matter of processing power, not the camera sensor.
There's still no expandable storage, which is a bummer. You're stuck with the 16 GB internal storage that isn't even accessable on a computer or car stereo as a USB mass storage device.
So What's Missing Now?
The Galaxy Nexus is the first Nexus I actually bought. After using it for some time now, I have to say I like it. However, I still LOVE LOVE LOVE my Galaxy S II. Aside from display, NFC, and stock Android ICS envy, the Galaxy S II has everything the Galaxy Nexus have and more!
To round out the Galaxy Nexus, I would have liked to see expandable storage (micro SD, please!) and better camera (use the Galaxy S II's sensor, please!).
I find those as major parts of today's smartphone experience! The storage issue is a huge part of Android experience especially (Titanium Backup and ROM flashing addicts).
Of course, the Galaxy S II has it's list of shortcomings as well, but it's mostly software-related (things that stock Android ICS won't have).
The search for the 100% perfect phone still eludes me. I guess it would only be perfect if I made one myself. And even then, it'd only be "perfect" for me, myself, and I.