Because most Whovians from the original series hated the 90's TV movie. McGann is amongst the least liked TV doctors. It is ironic since he is the favorite Expanded universe Doctor. So there is a faction in Who fandom that love him for Radio Dramas, Books, and Comics. The rebooted show has even used lore from that horrible TV Movie and the Books. But Both Moffet and RTD have made it clear that the TV Movie is non-canon, but McGann was the 8th.
So why A new actor to play the Time War incarnation, because the 9th was just off a Regeneration after the Time war, and the 8th most likely was at the start He also was the only Doctor to be born from a Gun Shot.