Some modest spoilers for John Wick and John Wick 2 below.
The biggest mystery of the John Wick films has nothing to do with the titular hitman's seeming invulnerability. It has nothing to do with his origin story. It has nothing to do with the provenance of the doubloons that serve as the coin of the assassin's realm, nor with the fact that virtually everyone around you, according to these films, has a silenced pistol at hand ready to take you down.
No, the central mystery of John Wick and its sequels is far simpler: Why does Winston, the proprietor of The Continental, call John Wick "Jonathan"?
Look: "John" is not short for "Jonathan." "Jon" is short for Jonathan. John is short for nothing, John is just a name unto itself. Something is amiss here.
As best as I can tell—because I'm just spitballing here and finding out would probably require something like putting in a phone call to screenwriter Derek Kolstad; ain't nobody got time for that—there are three possible reasons.
1. It was a flourish by Ian McShane that the director left in
My working theory after seeing the original was that this was just a little flourish added to the character Winston by Ian McShane.* The idea was that this is how a posh older Brit would refer to Jon, by his full name, and that McShane just didn't realize the whole John/Jon problem.
But then I found an early script of John Wick—so early it was still called Scorn—and realized that, well, it was there all along:
2. This is how The Continental shows its dominance over Wick
So, it wasn't a mistake. It was intentional. Interestingly, in John Wick 2, the manager of the Roman branch of The Continental also calls John Wick "Jonathan." Everyone else in the employ of Winston and Julius (Franco Nero) call him "Mr. Wick," as far as I can remember. But the bossmen—the men with the power to revoke Wick's membership to The Continental and deny him its many life-saving, life-extending services—call him by a malformation of his Christian name. Interesting, no? Perhaps this is a subtly domineering play, a way of reminding the assassin that even John Wick, first in class, bows before a higher power.
3. A gaffe designed to mirror the film's anachronistic touches
There's a weirdly pleasing dissonance to the John Wick universe; it is, after all, a world where a room filled with old-school switchboard operators send orders for hits typed on typewriters to each other via pneumatic tubes so ... the message can be blasted out digitally to thousands of cell phones all at the same time. It's a world where gold coins are exchanged as tokens of honor among thieves who receive millions of dollars for jobs completed. It's a place where time has no real meaning, where ancient ideas mix with modern weaponry seamlessly.
So maybe the whole "John/Jonathan" bit is a way to extend that frisson. I dunno. The point is that John Wick is great and this is just another level to its greatness.
*McShane also played the devilish Al Swearengen from Deadwood, the best (or possibly second-best, after The Sopranos) program HBO has ever produced. Save your "but THE WIRE wah wah" for someone who cares.