Please note that, m2e-wtp and Sonatype's m2eclipse-wtp overlap and can not be installed together.
if you try to update your Eclipse installation via "Help > Install New Software...", m2e-wtp won't install because of the conflict with m2eclipse-wtp (this is a bug in p2).
if you add the m2e-wtp update site to your list of Available Update Sites, doing "Help > Find Updates" should find m2e-wtp as a suitable replacement for m2eclipse-wtp, and everything should update properly.
The safest path to upgrade is to start from a clean Eclipse installation. Good thing you just downloaded Juno SR1 right?
Oh, by the way, JBoss Tools 4.0.0.Alpha2 and JBDS 6.0.0 Alpha2, coming in the next few days, will be compatible with m2e-wp 0.16.0.
The project is still incubating at the Eclipse Foundation, while we're working on stabilizing it, its API and working on new features. We're hoping to make m2e-wtp part of the Kepler release train,
and why not, integrate it direclty into the Eclipse Java EE distribution next June.
Finally I'd like to give some kudos to the WTP team from IBM, who was really instrumental with the project migration to eclipse.org and who also provided several patches to m2e-wtp.
I'm confident that, together, we'll be able to greatly improve both m2e-wtp and WTP itself.