Except at some point between The Last Stand and The Wolverine, Professor X somehow managed to completely mutate that man's body into an exact physical double of his former self. He took a middle-aged man, stole his body, and aged him 40 years. And unless that man was paralyzed as well as brain dead, the professor also saw fit to sever his new body's spinal cord for reasons that we will never be able to understand. Maybe he'd grown so used to the wheelchair, he just forgot how to walk.
And it's not like we can chalk that up as a non-canonical scene that was thrown in after the credits for fun. When Days of Future Past begins, Professor X is totally still hairless and in a wheelchair, and nobody addresses it. He successfully assimilated another human being, body and spirit, and this never manages to come up in conversation.
20th Century Fox
"My God, does this mean Cyclops could have made it back, too?"
Also, at the beginning of The Last Stand we see that Professor X is walking around and totally friends with Erik in 1986, when they go meet Jean Grey as a young girl at her parents' house. So that means he's still secretly juicing on Beast's power-dampening serum from Days of Future Past, operating at half of his psychic ability for the past decade or so just so he can strut around in a pair of dapper trousers. Constantly dosing that miracle drug must be the reason why he went from looking like Lieutenant Dan to Telly Savalas in the span of 13 years. Although Beast himself apparently forgot all about the serum, because by 2014 he's just furry blue Kelsey Grammer 24/7.