Roy wasn't removed because of popularity. He was removed because of his utter worthlessness to FE (That's subjective, but follow me here). Both Marth and Ike are much more representative of the series. Roy was advertisement for the new FE game that was released in Japan at the time.
I do agree that Ice Climbers tend to be disliked by casuals. They take a lot of work, and are frustrating for people who just play as them once in a while.
Perhaps the same reason why Sheik is so popular in every crowd. She's easy to use and "master" on a casual scale, if you decide to pursue competitive status with her, she's also extremely good.
I would have personally be very saddened if G&W was removed. He has a very unique and very Nintedo symbolic moveset. Pichu, Roy, Mewteo, and Dr. Mario were none of those things. Well, Mewtwo was fairly unique, but Lucario is 4th gen, and slightly reminiscent of Mewtwo anyway.