I'm not sure I can think of a series that needs a reboot, in the sense that the word is typically used. Mario already kind of had one with New Super Mario Brothers, and then it stuck with that style over three more games. It isn't a "reboot," but I'd like to see more variety in Mario games again. Zelda games have always seemed distinct and unique to me, even something like Majora's Mask which uses the same engine and graphics as the previous game still manages to feel completely different, so I currently have no qualms with Zelda. Metroid has just had one misstep with Other M, and maybe a little with Fusion. But both those games have good qualities too, believe it or not, so I don't want them thrown out entirely.
I can think of things that I would want to come back, like StarTropics, Battalion Wars, the Excite series, etc., but that kind of thing isn't a reboot.
The only thing that's coming to mind that might qualify is Pokémon. I don't know if I necessary want a complete erasure of everything and starting anew from the ground up, but this series has just gotten too convoluted and formulaic for my taste. When I have felt like replaying a Pokémon game, I instead played the next newest one in the series, that's how samey they are to me. I've never liked any of the new stuff they added since Gold/Silver, such as the EV/IV stuff, natures, abilities, etc. I'd like to see the series made simpler and more user-friendly. I'd also like to see more done with the story, I think there's a lot of interesting things they could do with this world, but it's always about simply becoming a champion because it's the cool thing to do, with a little bit of random bad guys or legendary origins thrown in here or there, which is usually stupid.
Now that said, I haven't played Black/White yet, and of course X/Y is due out soon. So I can't speak on those, no idea if they are getting closer to what I want.