Backups normally have miscellaneous settings and code from previous OS versions. It can cause kernel panics and miscellaneous problems. For most users, this won't be an issue but after enough usage and OS versions, there will be a lot of data left in the system that is classified as miscellaneous and can cause problems. iCloud backups seem to be a little better than iTunes backups. If you're looking for flawless performance from a new device, the best practice is a clean install. If you care more about saving time with apps and data, restore from backup. If you then run into issues, do a clean install.