I'm in awe with the game and I play it rarely, bits by bits, so it lasts longer, so I try to count every single chapter.
How deep in am I?
You can go to Skellige at about 5% of completion. The game is set up in a way for you to find Ciri by doing a bunch of different quests around all parts of the game world.
Just because you went to Skellige doesn't mean you have completed anything except the tutorial area and unlocking Novigrad.
There is no way to assume how far you are just by being in Skellige.
I often think about the main story line of the game in terms of Chapters.
It's not explicitly stated, but Ciri's personal story line seems to run in this order: Skellige Forest -> Velen (Crones -> King of Wolves -> Cocatrice) -> Novigrad -> Skellige Town
Cure Uma.
Retrieve Ciri from her hide-out & The-Big-Fight Pt. 1. Prior to starting this, you'll be asked if you really want to. Ask yourself, have you collected on all available Debts?
Of course there is much more to the game than just the main story line. Rich side quests & points of interest are really not to be missed.
If I can remember right it's the third our of 3 main zones. So 66%.
https://gamefaqs.gamespot.com/boards/702760-the-witcher-3-wild-hunt/72421500 Gamespot gives it about 60-65%.
That is only counting the main game. There are 2 DLCs that would be about the size of a zone. So if counting with DLC, about 40%.
Surely there are other ways to tell, e.g.: how many hours have you played? Divide that by, oh, say, 250.
That is: if you are really enjoying The Witcher, and you continue to enjoy it, it's quite likely you'll spend hundreds of hours playing it.
I believe I spent nearly 200 hours playing it, and I certainly wasn't finished by then.