I figure Roy's popularity in CYL was heavily influenced by Smash, at least in the west. The boy is fairly popular in Japan, I think. But Awakening also greatly increased the series' exposure to the general Nintendo fanbase, and a lot of those players probably carried over a lot of the "our boy" sentiment.
Ike, however, has just always been the second coming of Hector. A blunt but good-hearted warrior with no penchant for noble affairs, who also grows into their role and becomes a beast of a unit, that was sure to be popular. As a western fan, he especially stood out to me because his game was the first we had where using the main character in battle began to feel less like a massive escort mission, and his prowess in combat made it seem like he deserved his role as the protagonist.