Scrappers walk into a group of enemies and start wailing away. Stalkers invisible move up to the strongest enemy, use their version of assassin's strike to take him down before waling on the rest of your opponents. Stalker sets have to replace one of their primary strikes with an assassin's strike, sometimes that's an improvement, sometimes it's a loss. They also have to replace a secondary power with hide, again with mixed affect on the power of that armor. Stalkers also have placate to temporarily go invisible again, while scrappers have confront to taunt an enemy. Stalkers have slightly fewer hit points and I think scrappers do slightly more damage in a straight up fight. In short, a stalker and scrapper can end up playing quite differently even if they have the same primary and secondary.
Edit: Also, scrappers have follow up, an attack that improves damage of subsequent attacks for a little while, whereas stalkers have build up which is a self buff that improves damage and accuracy for a little while.