What is the problem with the wtp directory structure ? Maven supports having multiple projects.
Anyway you can enable JSF support on normal projects too; just not sure all features will be enabled because arbitrary project structures won't contain all the information needed to work.
In any case, there is nothing magic about our tooling compared to eclipse - how would you do projects in a team with eclipse anyway ?
I do it by having multiple projects for each larger module (just like maven) and maven even supports generating WTP projects BUT unfortunately that doesn't enable our features so I recommend using the maven eclipse:eclipse generation initially and then use eclipse to adjust the project/classpath and settings that eclipse knows about.
But yes you will need to use ant or maven to write the build scripts - nothing different from normal eclipse.
Note: we will look into automating these things in the future, but for now we rely on that both ant and maven can work with Eclipse as is.