I think the basic question is, do you want a U3 drive or not? You can remove U3 but, if you do, I believe the U3 programs will not work. After all, they were designed to be U3 versions of the software.
If you're going to keep U3, then do not delete the Documents folder on your flash drive. You can create folders on it, same as you would a hard drive. So, if you want to store files in a folder other than Documents, no problem.
If you want to remove U3 from your flash drive, you can still install portable versions of many programs by downloading them from portableapps.com.