Mario is, undoubtedly, the more popular of the two. As the Colonel put it in one of his conversations with Snake in Brawl, "There's probably not a single person int he world who doesn't know who he is." Mario is an excellent example of how a semi-childish series can go right in every way. However, while Mario is Nintendo's flagship franchise, it is not as important to them as Zelda. It really isn't, despite what you may think. Mario has had its share of screw-ups (like some of the sports games out there) and it has had its share of gems (nearly all console games). But you know Mario's classic "duduh duh duduh DUH! duh"? What if I told you it, while undoubtedly the most recognized video game song ever, has not been included in every Mario game? It's true. Super Mario Bros. 2 (Doki Doki Panic in Japan) didn't have it, Super Mario World didn't have it, and a lot of the Mario Kart games haven't included it.
In comparison, Zelda is simply more well-received. While Mario is Nintendo's flagship franchise, Zelda is Nintendo's baby. Their games are definitely the most well-done, and Zelda has been ranked as the number 3 game franchise in history (behind Call of Duty and Halo, which I believe are not worthy to hold up the jock strap of Link, due to the fact that most people only buy those games so they can play online multiplayer), In fact, in a Deathmatch tournament between Zelda and 15 other Franchises, Zelda came in first by beating opponents in this order: Star Fox, CoD, Halo, and Mario. I'll try to find the link (no pun intended) to the tournament thingy in question so I can prove it, but it'll be a little hard, so bear with me. You know the theme of Zelda? Unlike Mario's classic theme, the Zelda theme has appeared in literally every Zelda game somewhere. Just goes to show which franchise Koji Kondo cares about the most.