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The short answer is yes it's worth it, because it gives you the flexibility to install apps that make the experience much better.
You asked several questions I'll try to address them.
Kindle 4 Android vs nook
Personally I think these clients are on par with each other. They offer the core features needed to be useful. Search, dictionary(nook is better), notes, highlight, bookmarks, Goto page/Goto location, and table of contents.
The nook however has margins, fonts, and line spacing, but they are predefined to three and rather useless for me. Only the font selection is a real feature. The kindle default values are more to my liking(no margins and single line space). But I'd image it would be hell for those who don't like those settings.
Kindle 4 Android (K4A) vs Kindle 2 (K2)
I have the K2 and would say the K4A is a better experience for me(software wise). The only thing the K2 offers over the K4A is TTS and margin control. A side from that they offer the same functionality, but the K4A is designed for a touch screen which makes interacting with the software much easier. Adding notes, highlights and page turning are much easier and have less ware on the device.
K4A vs nook vs Other android apps
Here is where the nook and K4A fall on their face. There are some really nice reading software that exist on the android platform that are far better than the nook and K4A. They offer true magin control, font selection, line width, paragrah indentation, etc... In addition to TTS.
Moon+ Pro is my choice of reader when I'm not using the K4A and is by far the best. My reason for using the K4A is like you I have a lot of books and read on different devices like my smartphone and Kindle. Whispersync really makes sync between devices a breeze. Also I understand Kindle(MOBI) annotation system and it is easy for my to transfer my highlights, notes between devices.
As far as the nook rooting experience.
It is no where near as good as a polished tablet experience, there is missing core software and missing standardize functionality that B&N has removed to give their flavor If your goal is to be productive with the nook you will be greatly disappointed.
However rooting the nook has allowed me to install Moon+, ezPDF, and Kindle. Moon+ and ezPDF are light years ahead of the default apps. This has made the nook color a great reading experience. I've also updated the browser to dolphin and browsing is awesome and installed K9 the best mail client on the Android platform.
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