Upgrade. I've only ever done a fresh install of OS X once whereas on Windows upgrade was for crazy people. I actually upgraded last year from the first beta to the official release and there were zero issues. As always, backup first.

Depends on which category you fit into.

You use dev tools and stuff like homebrew/macports a lot: fresh install is a lot nicer.

You don't use the above that much: Upgrade is fine.

As for the packages, I had a lot of different packages that were built for Mavericks, and needed updating, and would constantly bump into something new that needed something reinstalled etc. Various reasons for this, like Apple moving around system utilities and upgrading various things.

EDIT: Just to be clear, all is solvable with the upgrade. It's just a bit cleaner with a, well, clean install ;)

I experienced no problems with earlier major OS X updates on my MBP, so personally I'd go down the update route. Nevertheless, it's a good idea to have Time Machine backups at hand.

Upgrading works surprisingly good. I never ran into any issues if I recall correctly. For me however, this one is going to be a clean install. I do them every 2-3 releases.

I am old school. Across major versions, I back up my files, create the install media, and clean install from that.

By the way, Yosemite runs really well on my MBA. The only thing that bugs me is the hideously ugly folder icons.

I always do a fresh install. I save backup of my $HOME, but don't restore it (I copy what I need when I need). It's perfect time for getting rid of old unused applications, projects, etc. But it takes time and patience.

Strange, I guess I'm an outlier but I always do clean installs for a new OS.