Hi,
If you do inplace upgrade, you dont need to deploy your content/packages or bundles etc. You dont need to reconfigure any custom authentication or any other configuration you did in the older version like logging or schedulers etc.
so inplace upgrade will save a lot of effort.
if you do a fresh install of aem 6.x version, you need to deploy everything again.
You need to migrate the repository only in case you are upgrading from AEM 5.6.1 to 6.1/6.2/6.3
if you are already on 6.1 ,no need to upgrade repo., you just need to run 2 commands and its done.
choice is urs, 2 commands or 20 commands.
Few advantages,
a) Fresh instance without any orphaned version histories (GB's of data under /jcr:system/jcr:versionStorage)
b) No worries on the versions of the bundles which would not get upgraded and will stay as only installed state.
c) No chance of old legacy corrupted nodes continuing to stay in the upgraded instance, since this will be brand new.
d) Avoiding any extra manual steps which are involved in cleaning up of few files from the launchpad location as documented in my in place upgrade blog.
e) Lesser chance of indexes getting corrupted.