Would you enjoy it if you beef up your character, spend hours training him and improving his stats only to find out that he's actually the bad guy and that he will be taken from your control, replaced by a new character and you have to compete against the character you pumped up? Frustrating. Not interesting.
Speak for yourself. I think this would be a tremendously cool plot twist. Imagine a Star Wars game in which you played Anakin, up until he becomes Darth Vader, then Luke is introduced and you start playing as him. Or any other plot along those lines.
"The following is not for the weak of heart or Fundamentalists." -- Dave Barry