Buying should warrant bonuses, but should not be the base for points. In the manga section, the entire thing requires you to buy manga or you don't score anything. There are so many anime/manga that are still untranslated officially, so making buying a condition significantly narrows the scope.
I agree about the archiving. It should have lower points, like 100 per 50gb, not 500. It still matters though since it takes up disk space or dvds, which also cost money.
I also think the anime watched or manga read section should be extended, up to maybe 1000+, with a considerably higher score awarded as it goes up (just like how it jumps from 1000 to 3000 in the 100 and 200 ranges). This should be the focus in fact, since how can you be an anime otaku without watching anime? It also shows how much time you devote to the hobby.