Well, well, well, allow me to enjoy the big helping of schadenfreude that the TVD writers have so considerately served me.
I spent the hiatus after the Doppelganger!Stefan reveal dreading it portended some kind of mystical bond between Stefan and Elena that would make them Soulmates or something, which was about the last thing I could want.
Now, however, it turns out that there is a mystical bond between Stefan and Elena, but it’s a bond shared by umpteen doppelgangers across the millennia, which makes it totally ok and in fact kind of great.
Because Stefan and Caroline and hordes of Stelena shippers spent last year bitching and moaning that of course Elena only was with Damon because of the Sire Bond, she would never want him otherwise, she was pulled to him against her will, supernatural forces were manipulating her and if only the Sire Bond could be broken she’d return to her correct Team Stefan Original Factory Settings.
Now it turns out that those Team Stefan Original Factory Settings only existed because of… drumroll… a mystical Doppelganger Bond that is not even as rare and dependant on pre-existing feelings like a Sire Bond, but something that has happened to dozens of doppelgangers before them simply because of their doppelganger natures.
Basically "The Epic Love of Stefan & Elena" is actually "Silas!Doppelganger #275 & Amara!Doppelganger #275: The Umpteen Remake".
“It [was] always going to be Stefan” both for Katherine and Elena not because Stefan is OMGSoDreamy!11 but because as doppelgangers of Amara they were freaking programmed to be drawn to any and all doppelgangers of Silas they encountered.
Otherwise said, I’m pretty sure Stelena cannot possibly be endgame, for the same reason everyone knew that Elena was going to choose Damon in the season 4 finale: everyone was talking about how she would choose Stefan, so what would be the point of that happening? Same here: if Destiny pulls in a direction, where is the drama in making Destiny win?
What is more compelling: watching a couple be together Because Destiny Says So or a couple being together despite Destiny?