That's actually not true. That plug is commonplace on a lot of music equipment, DJ mixers, etc. that are still manufactured and used commonly today.
I figure there has to be some reason for it in an age when companies are constantly cutting costs.
I doubt many people are trying to drive HD-650's with a phone anyway.
But I believe there's no difference in listening experience. The bigger plug is probably a lot sturdier though. I've had some 3.5 mm jacks bend on me. Can't imagine that on the good ol' 6.3. I have totally busted a 6.3 mm to 3.5 mm adaptor though.
For very long cables or high RF you might want a kind of cable called "balanced", which comes in every size except 3.5mm. Some audiophiles think these make headphones sound better, but it's probably not true.