Sometimes Maven takes heat for being "opinionated" and wanting you to do things a certain way. Even though it is usually configurable, it's normally easier to go with the flow.
It seems that the "Maven Way" is catching on, as masses of Maven users rebel against MyEclipse's attempt at using M2Eclipse as the basis for their Maven integration. In the beginning it sounded like a good thing, using the best plugin as a base to provide integration to more users. The trouble is that this implementation changed some core functionality and only supports new projects. Worse is that existing M2e users get tripped up by the incompatibility with the Maven4Eclipse implementation.
A key tenet of Maven is that all Maven based projects behave the same regardless of where they are. Once you know Maven, you should be able to work with any Maven project in seconds. It seems that MyEclipse broke this tenet and the users aren't too happy about it.
A more appropriate approach would be to work with M2e to add features instead of effectively forking it.
You can read more about it on Jason's blog.