I don't think you can really compare these games as they are just so different. First of all, Mario was made during a whole other era in the gaming industry, in addition to that it was made for a whole different platform and it was made by Nintendo, the one of the biggest gaming companies in the world, against Lima Sky, some independent game company.
And let's not forget the fact that both games are entirely different, with entirely different game-play, goals and styles.
If you really need to have a choice, it'd be Mario as it actually contains a lot of story line, but it'd mostly be the nostalgia that would make it better in my opinion.
Nonetheless, I don't think these games are comparable and it seems rather silly to ask a question like that, it's like asking what I like better, reading a magazine or watching the news.