You're forgetting that Mother 3 hasn't been currently released like Earthbound/Mother 2 has/will be.(again, I forget).
I think that could play a role if he only can choose one. But remember, I doubt either would leave, but if one had to, it'd be Lucas easily. Ness has more staying power in the end.
And I don't know which is honestly more popular. I think Mother 2/Earthbound is better, since I am not a fan of that musical-based(twitch-action rpg's) gameplay. Basically, while I like something via Paper Mario's, where you do a bit of Action Commands, I don't like when it becomes the entire gist of the battle system where it's severely affects it, like in Sonic Chronicles. Paper Mario isn't the best example, I admit. You do need to be good at them to win in many cases. Super Mario RPG is perhaps slightly better. If you suck at Action Commands, you can still pretty easily win the game, since it's not super hard enough to punish you greatly if you fail.