Truth be told, I'm not super far into Earthbound (Pretty much at the second guardian) but besides that point, I've always loved Ness/Earthbound for the story and how it's told, while I haven't progressed really far in the game, I've seen some youtubers who've played through the game and found most of the information about it from watching gameplay and I really loved the experience, a funny YET serious story about a kid's life and how he and three others are going to save the world.
I first experienced Ness as a character in general in Smash Brothers 64 as EU never saw a release of Earthbound until the Wii U VC release, I found his gameplay unique, a little hard but I kept growing into the playstyle and he was my main back when I was a wee kid, Ness is still my main used character in the recent Smash Brothers to this very day, I STILL enjoy using Ness and it hurts me to know he's been considered a really spammy character in the game.
Sorry if it's not all a good reason to call Ness my favorite since I haven't played much of the main series in general (I haven't even touched Mother/Earthbound 0 or Mother 3!) but I feel comfortable with calling him my favorite, not to mention that Ness' design is just absolutely adorable, a hat REALLY can make a kid look adorable.