Unlike previous grid control installations, Cloud Control separates out the database software installation, so you have to do that installation first, then install Cloud Control against it. The process is shown here:http://www.oracle-base.com/articles/12c ... -and-6.php
That in itself should not stop you from considering Cloud Control. I assume if you are comfortable installing things like Grid Control and Cloud Control, the thought of installing a database is not a problem.
Just because it is a separate installation step, does not affect the licensing of the product. You can still install it (DB and Cloud Control) for free, provided you are using it to manage fully licensed Oracle databases. As long as you don't use any features in CC that you have not paid for in your managed databases, you are not breaking any license agreements. Also, the DB and WebLogic installations can only be used for CC. You can't have any of your own apps hosted by them. This is essentially unchanged since the 10.2.0.5 situation.
I see little point in holding back from 12cR2. There are no technical reasons to do so. There are not licensing reasons to do so. It's actually easier to install than 10.2.0.5.