Mike,
Interesting, what happens when you have developers who are not using MyEclipse?
Not an issue here; I work for a very large company that has been standardized on it for quite some time (happily, I might add as we used to be a WSAD shop -- shudder.)
Anyway, if you have some that use MyEclipse and some that don't I see two options. First, if you create MyEclipse web projects and then "Add Maven capabilities" (or whatever it's called) to them, they'll work in MyEclipse and from the Maven commandline as well. So even if you're not using MyEclipse you can still use the commandline Maven tools. Also, since the MyEclipse structure is the more standard "exploded war" layout, it should work with whatever else you use as well.
Other thing to consider is that Maven's web layout is simply a default and Maven can easily support any project structure, including the one MyEclipse uses, so you should be able to use the MyEclipse project with Maven in any tool with just a little additional config. That's likely why the Maven commandline tools still work on the MyEclipse Web projects -- the MyEclipse guys just automatically configure Maven to recognize the format.
You also could just import the externally created Maven web projects as I said in my last post. We don't like to do that because that structure is unique to Maven and just doesn't work with any tools except Maven. As a result, it basically defeats the the tool support you get automatically in MyEclipse, Eclipse Java EE, or pretty much any other tool. It's just a poor default. Exploded WAR format, that's used by MyEclipse, Eclipse Java EE, WSAD, RAD, and everyone else is simply a better solution. Especially when it still works with Maven just fine as well.
Maven was made to be flexible to project structure. We've just found by using that flexibility a little you can get Maven support and great tool support too.
Dave