The features of SuperContainer and Native FM Pro 12 are not identical. You'll need to review the needs of your users and check them off against the "feature list" for each option to see if FM 12 alone can do what you need or not.
A particular concern is if you will use IWP and need for users to be able to upload files into container fields or not. I believe SuperContainer offers teh ability to do that where you can't do it with just FIleMaker 12.
Thanks for the tip, PhilModJunk.