One of the main advantages of wubi is that you do not have to repartition and then can uninstall it with Windows and recover all the file space. It exists just as a file (root.disk) inside the Windows NTFS partition.
If you have a separate partition, it really is better to do a full dual boot install to that partition, even the developer of wubi expects you to do that.
From the developer of wubi:
Agostino: Wubi actually wasn’t designed to do long-term installations. The main aim was really to let people try out Ubuntu with confidence. Normally, users that start with Wubi tend to upgrade to a full installation to a dedicated partition at the next release cycle.
More info on wubi: