Use time Machine back up to upgrade or fresh install of Mavricks

New versions of OS X are designed to install in place of your existing OS. There is no advantage in doing a clean install.

1. Most users, after doing a clean install, will migrate their entire user account, apps and settings back anyway. Assuming you have some problem in these elements, then you've brought it over again. At best, you've emptied your caches and deleted your temp files, but done so the long way round by deleting everything and restoring everything except those.

2. The alternative strategy might be to do a clean install and then selectively restore things from your backup. Well, if you know which files you're going to restore, then you can again do the short version by only deleting all your files that aren't in your list. That way, you just delete a small fraction of stuff, rather than deleting everything and replacing a large fraction of stuff.

So you don't need to use the Time Machine backup at all. However, your Time Machine backup should be an identical copy of your files. If it's not, then that's not a backup.