In the light of the most recent hints, it seems clear that the pair we are actually looking for is
Harry Potter and Neo from The Matrix.
Here are some details.
We two were the ones
destined to do great things
There was a prophecy and all.
We started as did Jon
aware of Nothing
At the start of Harry Potter and the Philosopher's Stone Harry is living under the Dursleys' stairs and has no idea magic is real. At the start of The Matrix Neo is still called Thomas Anderson and living in the Matrix, and has no idea (beyond a few un-understood rumours) of what his world really is.
A world we didn't know
turned out to be our home
For Harry, the world of magic and wizards. For Neo, the world outside the Matrix.
Waited where we were
with glorious foretellings
While everyone believed
we thought ourselves a regular Joe
Otherwise the future revealed
A destiny for us each
There were prophecies about both: Harry was "the one with power to vanquish the Dark Lord" and Neo was "The One" who would save Zion from the Machines.
Closer to our nemesis
than others we were
Harry is Voldemort's accidental horcrux. Neo has a ... curious ... relationship with Agent Smith and ends up getting "assimilated" by him.
Entwined with their life
Our deaths were
Harry was killed by Voldemort, with the intention of getting rid of the extra horcrux. And of course his death had ... further consequences ... for V. Neo sacrificed himself to Agent Smith, rather more finally, in order to destroy Smith.
I marked him, He marked me
In H.P.'s case, "the Dark Lord shall mark him as his equal". In Neo's, "I marked him" points to the climactic scene of the third movie where Smith assimilates Neo. (It would not be difficult to find "I marked him" candidates for H.P. or to describe that same last scene as "He marked me" for Neo.)
The death of them, incident seemed to be
But not all was revealed
to the four of us it was
A great transfer of power
though unintentional it was
In H.P.'s case, V. was thought (by many) to have died when he attacked H.P., but that wasn't really the case; in the process of what did happen he transferred some of his powers to H.P. In Neo's, Smith thought he was assimilating Neo and taking over his powers, but the poor chap found that that wasn't quite what happened.
Helped us to the end
our mentors did
But not everything of our end
tell us they did
Their own end they met
too very soon
But even then a part
remained to be seen
Dumbledore was (intermittently) helpful to H.P. from the beginning until his death, and even afterwards (his will, his instructions to Snape, and "King's Cross Station". Dumbledore didn't tell Harry himself that he would have to die or why (he let Snape do it, which ended up happening in a rather roundabout way) and didn't tell even Snape that he expected Harry to survive his own death. This stanza confused me before when I wondered about The Matrix, but it turns out to be a reference to the Oracle. To be frank I'm not sure she really counts as a mentor; but indeed she gives Neo some important advice, she doesn't tell him (anything like) everything, she dies (maybe?) between the first and second movies but appears after that, she dies (more completely) when assimilated by Smith, and (thanks to the OP for pointing this out; I'd forgotten) after the Smith-Neo fight it's her body rather than Smith's that's left lying in a ditch.
Alone at last
against our enemy we were
Sure of our fate
we sacrificed ourself
H.P. in the forest, getting kedavrified by Voldemort. Neo in the third movie, getting assimilated by Smith.
Similar though it seems
Not the same it is
Because here at the end
the difference is revealed
I was resurrected,
But I couldn't do it again
H.P. returns to life (or maybe never actually quite dies) in the forest. After this he is no longer a horcrux and if killed would just be boringly dead. Neo isn't (so far as we can tell) resurrected at all in any way after the events of the third Matrix movie.
I didn't know him, he didn't know me
A verse different we turn out to be
Our two heroes are from different fictional worlds.
Before/after the end
our mentors did reappear
Dumbledore has a chat with Harry in "King's Cross Station". The Oracle reappears as a corpse in a ditch.
Do guess our names
Please do it dear.
Harry James Potter, a.k.a. The Chosen One and Thomas "Neo" Anderson, a.k.a. The One.