The pilot that eventually aired on HBO is not the original one created by Dan Weiss and David Benioff. Both have spoken at length about how bad the unaired pilot was. Weiss even said that watching it was "one of the most painful experiences" of his life.
George R.R. Martin actually took a page out of Stan Lee and Alfred Hitchcock's books by making a cameo in the pilot as a nobleman at Daenerys and Khal Drogo's wedding. Too bad we'll never get to see it.
Emilia Clarke doesn't even play Daenerys in the pilot; she's played by Tamzin Merchant (Salem). While the reason for the recasting was never revealed, Martin commented on his blog that he thought her performance was "wonderful."