We have found a bug in the project creation using the PhoneGap runtime of 3.6.3 that causes the new PhoneGap Project creation to fail.
The current workaround for this is to create the project using 3.5.0. You can then change this by right clicking on your projects root folder, select Properties, then goto MyEclipse>Targeted Runtimes and change it to your needed runtime.
We are working on a fix for this and hope to have it available soon.
Please note this only affects the underlining command line interface and will not affect the PhoneGap version referenced in your config.xml file. You will need to manually change that if you wan to use a different version.