Alright, I can finally do the Latias and Latios mega stones quest after finishing my char x.
From what I got, you need to bring 2 pokemon, 1 which has fly as the move. Then, after talking to the professor in the first floor, you'll be in the Cloudy Path.
The first thing you will see is Latias and Latios together in the same place. Then, when you talk to any of them, you'll start a fight with them. After you beat the two of them, they will run away and you need to follow them. This goes on for 5 times, then you'll be faced with 4 lines.
I've done it twice, and they also pick the same path. I follow the path picked by the duo and I'm safe. Don't know if the path differ to everybody or there'll be anything happened if you pick the other path.
Then you'll fight them once again, they ran away again, but this time when you try to chase them, you got stopped by Emerald which use 2 pokemon; Volcarona and Mega Gengar.
After you beat him, go after the duo again and fight them again one more time. This time you'll see two path; one to the left, and one to the right. There's a sign before the left path saying something about greed, forgot to capture or write it out, and the right path is blocked if you haven't fight the duo in that place. This time, the duo is faster than my pokemon, they might actually grow stronger after every time you fight them. After fighting them, they run away to the right path. This time, you'll see them facing each other, the one you talk to will be the one who'll go mega. I talk to Latias, so Latias going mega in the next battle. After beating them, take your well-earned mega stones (yes, you got both at the same time) and you can go to the sparkly-thing in the end-path or try going to the left path, you'll never know what you will find there (literally).
That conclude the Latias/Latios mega stones quest