Migrating

Setup/Migration assistant is quick and easy.

Manually moving files is time consuming and tedious.

Setup/Migration assistant may move over obsolete files like old preference files and the like. But all these old files don't do anything bad. They don't slow down your computer and they don't use up significant disk space.

I have always used Setup Assistant. As a result I still have unneeded files from my eMac I owned from 2002-2005 on my iMac running 10.11 here in 2016. These files have never bothered me. Taking the time to manually move files in order to avoid copying these kinds of files hasn't been worth the time or effort for me.

But I can understand the appeal of a pristine, clean system uncluttered with unneeded old prefs files and the like. Only you can decide if taking the time and energy for that is worth it to you.

If you do decide to migrate, one recommendation I do have is to use Setup Assistant and not Migration Assistant. Setup Assistant is what you get when you turn on your Mac for the first time and you answer Yes when it asks you if you want to transfer files from another Mac. Migration Assistant is what you do when you answer No to Setup Assistant, and try to migrate from another Mac later after you've already spent time configuring your new Mac. In my experience, answering No to Setup Assistant to only do Migration Assistant later is almost always a mistake.

Migration Assistant has options to select what you want to move over.

1. Applications
2. Users
3. Other files & system settings

Applications are best avoided IMO, they can be reinstalled with the current version as you need them, otherwise this brings over many supporting files (Garageband loops etc).

Users is probably what you need, it does keep all the old preferences & other junk in your account (some apps keep supporting files in the user Library etc).

Other files & settings can probably be left behind - you may not need the old network config etc. It will include files that are stored at the base of the disk - but frankly this location is really intended for the OS, your user folder is really where your files should live (or in /Users/Shared for everyone to access).

If you do clean install, setup the Mac with an admin user that has a name different to your current user accounts. Login & launch Migration Assistant when you are ready. Migrate the users you need, after migration if you find the user account is cluttered you can delete the migrated user via the admin account & start over.

Personally I avoid Setup Assistant on any Mac that has been used for a few OS versions, too much junk is just not helpful, it fills backups & merely gets in the way when troubleshooting.

Manually moving files to a user account is tricky - the OS will lock some files when you are logged in & overwrite other files when you log out (mostly preferences), if you log out & use a different user for the copy process the permissions can get in a mess. It is not unfixable, just best avoided.