I'm new to this, but this is how I see it:
- CRXDE enables you to easily work with files in the CRX repository. The UI lets you add, remove, open, edit (etc) files.
- With Eclipse, you are not directly connected to the repository. You need to manually synchronize files on your files system with the repository. You also need to use Maven to build and deploy your apps.
So, CRXDE provides many conveniences, but with Eclipse you are more generally integrated with your current dev environment, which makes it easy to integrate existing files and libraries, Maven stuff, etc, into your CQ.
But I don't think you have to choose one or the other. You can use both.
Regarding the obsolescence of CRXDE....I don't know.
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I'd sugggest using maven and eclipse for your larger development. It seems to be better suited for larger teams, CRXDE and CRXDE|Lite seem to be more for smaller teams/single developers. A breakout into multiple projects is probably a good idea (one for design, one for an initial test content, one for code that goes into apps, one for a taglib if you don't want to use just jsp code and do scripting and maybe one for configuration settings).