Hi,
the first thing that comes to mind is that you will have to update your roles. There are many new authorization objects and checks in ECC 6.0 comparing to 4.7. So you will have to amend your roles accordingly using standard transaction SU25. The will be probably the biggest task and you can't avoid it.
The newer version provides some additional methods for securing SAP system (e.g. securing RFC connections). The easiest way is to go through SAP security guide mentioned by Andrea. There is also a separate document about hardening ABAP AS. That's a good document as well.
Cheers