You know how I made this post ages ago?
I actually think I got it... I don't know if it makes 100% sense, but I will try.
To understand it, we gotta go at the very beginning of the game, to Sherlock and Jon's first convo:
In this scene, Sherlock is unsure if the journey was worth the effort, because Mycroft believed nothing could be gained from it and his brother's words have gotten to him. Not only this, but he is sick and he likely senses that there is more to the journey than it seems. Jon, on the other hand, is certain that it's gonna be worth it.
If we assume for a moment that Mycroft was aware of how they felt as they took off - that Sherlock was still unsure about the journey even as he undertook it, and that Jon, on the other hand, was very much sure that it was the right thing to do, then from Mycroft's perspective, it would look like Jon was pushing Sherlock to do it. Of course, Sherlock wanted to visit Cordona as well, but it was likely Jon's influence that convinced him to actually get on a ship and do it. That's how it would look to Mycroft.
And since Mycroft humours Sherlock A LOT when it comes to Jon, he addresses Jon like one would address an actual person, whose influence has pushed his brother to do something he'd later come to regret.
He not only "I told you so"s Sherlock, he scolds him for not listening to him but to Jon. From Mycroft's perspective, it's Jon who is the instigator - he is the reason Sherlock is there, and he wants to know why.
Of course, this is only the superficial level. "Is he worth it?" is a very loaded question and Mycroft looking at Jon while he poses it is very intentional. He not only holds Jon partially responsible, he is also a little resentful, because Sherlock has, yet again, chosen to listen to his imaginary bestie over his brother. Is it far-fetched to assume Mycroft is jealous? Of course, Mycroft knows Jon isn't a real person, but the relationship Sherlock has with him is very real, and Mycroft is too smart to underestimate the influence Jon has. He doesn't have a body, but he has Sherlock's trust - something Mycroft has not. Not treating Jon like a real person wouldn't improve his relationship with Sherlock at all. Of course, Mycroft plays along! He is also smart enough to know Jon isn't just a piece of fiction - he must be aware that Jon is a part of his brother.
Jon, on the other hand, well... "Mycroft's nonsense still rattling around in your head" haha, yeah, Jon doesn't agree with Mycroft at all. He also asks Sherlock why Mycroft is there, because he is upset by the insinuation that he isn't worth listening to. They are two opposite forces in Sherlock's life, and in these two conversations, they both try to convince Sherlock that the other is wrong. Like the devil and the angel on one's shoulder.
I think we get a good glimpse in how their lives have been before Cordona - Sherlock always torn between reason (Mycroft) and emotion (Jon), but somehow always picking Jon's side. Yet still, Mycroft's influence over Sherlock is apparent as well, and the more he matures, the more Sherlock becomes like his brother. But the way there frustrates Mycroft a lot, because no matter how much he loves Sherlock, he can't get to him.
The whole "was it worth it?" question being posed at the beginning and at the end, but we don't get a direct answer. We can answer it for ourselves.
