Hi Asyraf,
It was a though choice, usually we don't go with deprecated features, but i dug up a little and discovered they can't really remove this feature without breaking many modules:
"Since the Module system is locked, this feature will probably never go away."
So after testing it on 0.11 we decided to take that little risk in favour of project simplicity. We would watch Node versions carefully to see if something changes ahead of a major release.
The naming is not the problem since you could just require your controllers like this: require('articles.server.controller') without relying on the extensions property, another thing is that we figured out a lot people use IDE look up(sublimes's ctrl+p, webstorms Ctrl+Shift+N, etc.) so typing your module name then narrowing down the list using server or client seemed like a nice touch.
It would be lovely if you could help people on this group and the facebook groups, another way to help the community is through PRs, which has great impact on the project development speed, many of the current features are made by the community(e.g., Express 4.x upgrade, Social account management, etc.), so this could also be a great way to influence.
Anyways keep us updated on what we can do to improve, what are you building with MEAN, and how we can help.
Thanks,
Amos