So am I to believe that the most popular Pokemon are in Gen 1 and 3, since most other generations got hardly anything even though every single non-event Pokemon is readily available? And Mega Rayquaza throws any semblance of balance out the window, it's the most broken Pokemon in the game since Gen 1 Mewtwo and all that needs to be said about the importance Game Freak places on balancing the games. So why did it get one? Because the one of the three poster Pokemon of the games they were remaking. Hey, Charizard, Blastoise and Venusaur got ones as well! Which coincidentally means that those six the only box art pokemon in the entire series that got mega evolutions.
So bring their anime personalities to the games? Brock is flirtatious, Misty is a tomboy; there we go as herculean of an effort as that was to attach those personality attributes so suddenly to existing characters in a game series so well known for its engrossing character depth I think I managed to pull it off well.