I liked both shows, but comparing the two can be difficult as X-Files has been off the air for years now and Fringe just ended recently. What seemed shocking, new and exciting on The X Files back then is not so exciting anymore. Many other shows have come and gone that were similarly shocking, groundbreaking, exciting, whatever. It's hard one thing against the other. I like them both, but Fringe went out early, leaving me wanting more, whereas X-Files went on for so long that it eventually drove me away. I think they are both equally good but X-Files covered similar territory/style first and was strong right from the start, while Fringe took a bit to get really strong.
However, I will agree that Walter is more interesting and likable than Skinner, Jose Chung & CSM combined. However, Fringe had the musical episode (*cringe*) BUT Fringe does get bonus points for this scene:
Walter's Acid Trip