This from https://wiki.debian.org/Projects/DebSrc3.0
Why should I convert my package to 3.0 (quilt) format?
* by keeping patches separate and properly documented
* the Debian changes are more likely to be reviewed
* any upstream contributor is more likely to find and merge the patches
(if you haven't forwarded it properly)
* other distributions can reuse our patches
* even if you don't have any upstream patch right now, next time that
someone must NMU your package, they can cleanly add a patch (with a
proper DEP-3 header) without having to modify the build system
* same applies for derivative distributions that have to modify your
packages... you're more likely to be able to find something valuable
to merge if their changes are kept as separate patches instead of
merged within the .diff.gz
* debian/rules can be simplified by getting rid of the
patching/unpatching code (or the uuencoding/uudecoding code if you
ship a supplementary binary file like an icon)
* the upstream tarball is bzip2-compressed and you don't want to have
to convert it
* the upstream tarball contains a debian directory and you don't want
to repackage it just to remove that directory
* the upstream author releases the software in multiple tarballs
* you don't have to add -i -I every time that you manually build the
package from the VCS repository (the VCS-specific files are ignored
by default)
* in the long run it's best to standardize on a single patch system (new
contributors need to learn a single system, more people can help you,
etc.) and quilt appears to be that patch system.