For a new project, Classic is the way to go right now. Classic and S will be maintained separately, in part because there will be no direct upgrade path from Classic to S. Their code and data model are completely different. So, if by 'compatible' you mean a direct upgrade (like there was from Omeka 1 to Omeka 2), that will not happen. On the other hand, if by 'compatible' you mean that both will be maintained, then yes, both will see development work.
There will, however, be a module for Omeka S to import content from an existing Omeka Classic site via its API. That's not a true direct upgrade, but it will grab large parts of the data from an Omeka Classic site and duplicate it in a new Omeka S site.