I think the difference is that the SF stories of the first few seasons tended to rely on a sort of b-movie adventure style and the novelty of the monsters and spaceships. With the historicals they just had people to write scenes for, and as a result you get a much more well-rounded and interesting story. I think the best Hartnells stories might all be historicals, actually - Marco Polo, The Aztecs, The Massacre, The Crusade. I think the only one that doesn't really work is The Smugglers.