I've like only watched the first 200 episodes of it (I know that because the last one I saw was like a 200th ep. special) and the only thing that added to the main story is that one of the member of the organization that Shinichi/Conan is after took the same pill that he did. So she also became a child and is helping Conan to get info on the pill and the organization she made so she can create a antidote.
Later on the story the former member of the oragnization Haibara Ai (its not her real name) developed a prototype of the antidote that Conan took and temporariely changed back to Shinichi just when Ran was catching onto the fact that Conan is Shinichi.
Thats all I can remenber for now so I'll PM you anything else I remember .