I never understood why he was not pardoned.
Nor I, and if what I've read is true, it was one of the few things Pres. Bush and VP Cheney disagreed on.
Although I don't know if Scooter is still pursuing an appeal, he was at the time. He wanted to clear his name. Scooter did not apply for a pardon. If President Bush had pardoned him, Scooter's appeal(s) would have ended without his having the opportunity to clear his name. I think time just ran out on all of them.