The fact that John asks “for me” at the headstone is just a killer, because it’s such a sad and pathetic plea. And it shouldn’t be selfish at all: you are, really, wishing that someone had their life back. But saying “for me” is an admittance of dependence and love and care that suggests that the desire is completely selfish: Please, Sherlock, don’t be dead, please, come back into my life, I need you.
And he says it twice, which is so sad, because the second time it’s so imploring. It’s like he is relying on the fact that Sherlock needs him just as much as he needs Sherlock, and that because of this and this bond and this friendship Sherlock ought to listen to him because it isn’t just anyone asking for this favor, it’s me. Do this for me.
What makes it worst of all, of course, is that Sherlock is dead and of all the impossible requests to make, it is this one, but John’s voicing it anyway, because he needs to. This quote is one of my favorites so I really shouldn’t have started talking about it but god, the phrase “one more miracle” — it’s the worst, the absolute worst, because he’s not asking for a miracle, he’s asking for another one. And the fact that he voices this gives credence to the thought that a part of him, no matter how small, does believe that Sherlock is capable of bringing himself back from the dead, simply because John is in that much awe of him. Sherlock isn’t a miracle worker or a magician, he almost always told John his reasoning and explained himself (eventually), and for John to ask ‘one more miracle’…
Well. It’s like an admittance that his entire acquaintance with Sherlock was a miracle, and it kind of was.
Not to mention what this is paralleled to, with the ‘please will you do this for me.’ The “keep your eyes fixed on me” order probably has something to do with the tricking John plan, which makes it all the more heartwrenching to think that Sherlock is imploring John to fall for the trick that will save his life (which explains Sherlock’s desperation). The requests are incredibly similar — Sherlock is just preventing John’s death instead of wishing that it never happened. And the real tragedy is that John doesn’t know. He doesn’t understand what this sacrifice means, and when Sherlock comes back he won’t fully understand how important, in the moment, believing the lie was. He’s going to walk around completely mystified by Sherlock’s suicide, knowing he’s been lied to, and totally oblivious as to why.
And Sherlock is so emotional on that rooftop. I really don’t think that that was part of the manipulation - perhaps to an extent, yes, but not fully. And it contrasts terribly with how stoic he is at the end in that graveyard, watching John. John complies with Sherlock’s request and Sherlock can’t — though, eventually, he will — and Sherlock becomes as impassive and connectionless as he needs to be to keep everyone out of danger, and to keep himself from feeling too upset about it.
So, in a way, Moriarty has won. His goal was to separate Sherlock from his friends, from the only people in the world who made him human, and he succeeded.