Well, I made a conspiracy theory as to why Roark and Silver look so similar.
But I'm going to start off with how I think Giovanni came to lead Team Rocket. (Yes this actually relates to the Silver and Roark theory.)
Okay so, I think that Roark and Silver are twin brothers, and Bryon is their biological father. Now in conjunction with the theory that states that Giovanni (Team Rocket boss) knocked up Mrs. Ketchum, I like to believe that before Team Rocket existed, Giovanni and Mrs. Ketchum were engaged and lived in Viridian City. Giovanni was the gym leader of the town. However, one day he devises a plan to become the strongest trainer in the world, but by doing so he would need to travel the world. At the time Ash's mom was fine with it and allowed him to go while she was pregnant with Ash. On his journey, however, he grows bitter as other trainers way younger than him manage to easily defeat him. Seeing pokemon as worthless tools, he distorts his dream and beings to devise ways of stealing the trainers' pokemon that have defeated him. He succeeds in stealing a few pokemon from trainers, but after a few thefts he gets caught and has his pokemon taken from him and released. He is later sentenced to a few years in prison.
Once he is eventually released, he returns home to his distant fiancee and his son who is only two or three years old. Thinking that she will support him, he tells her of his new goal in how he plans on using pokemon to take what he wants in order to become the most infamous pokemon trainer in the world. She is disgusted and ends up leaving him and taking their son with her. Distraught and embittered, he begins to form Team Rocket to fulfill his own dream with others who share the same ideals as him. As for the vague story of Ash's father as per bits and pieces of the anime, his mother tells him that he left on a pokemon journey and never came back, since the Giovanni she knew and loved came back as a hardened criminal. As his black market franchise really gets off the ground, Giovanni starts to feel lonely since he lost the love of his life and their son. Therefore, he takes another journey in a search to fill the void in his heart and life. (And to find a possible heir to his throne.)
His journey takes him to the Sinnoh region. And as he searches through Mt. Coronet for stronger pokemon, he comes across a miner and his two sons on a hiking trip. He watches the family closely and begins to take a liking to little Silver who constantly complains about going on such expeditions when he'd rather be off playing games with the other children in the park, or skipping rocks off of Lake Valor's surface. Roark on the other hand is so involved in what his father is saying and teaching about mining for treasures, that he pays little to no attention to his brother. Tired of feeling ignored, Silver wanders off on his own in order to sulk and toss rocks in one of the various groundwater pools. Giovanni remains hidden until Roark and Bryon are practically on the other side of the mountain before he forcefully kidnaps young Silver. Once he returns home, he begins to brainwash the young child and enlists him as a member of Team Rocket once he becomes old enough. However, Silver never could accept Giovanni as his father, and therefore easily disassociates himself from the group, but still holds to their ideals by stealing pokemon and treating others as targets or worthless. And once Red manages to defeat Giovanni's forces not once but twice, Silver begins to doubt his ideals and him altogether as someone who is strong and should be feared or respected. Therefore, he runs away to the lands of Johto in order to grow stronger than Giovanni and fulfill the man's dream on his own.
Now this is only a theory and probably has plenty of holes, but it makes sense to me. and it helps to link the games and the anime kind of seamlessly.
