If you ever plan on creating a new site, which starts off on a clean slate, especially with the WCM Publishing Features activated you must use stsadm to do that. Effectively three commands will get you started nice and simple with the most blank publishing site you can immagine:
a) create an absolute blank sitecolleciton with really nothing in it
stsadm -o createsite -url http://servername -ownerlogin domain\username -owneremail firstname.lastname@example.org
b) activate the publishing feature on the site collection level
stsadm -o activatefeature -name PublishingSite -url http://servername
c) activate the publishing feature on the web level
stsadm -o activatefeature -name PublishingWeb -url http://servername
That's it. go to your url and you will find the most minimalistic publishing site you will be able to get that has all the publishing features activated.
Now you can start building your own site template based on this and be sure that content deployment will give you less headaches should you ever decide to go down that route in future.