How come themes like BIONICLE can afford so many new parts? LEGO is quite economical about introducing new parts in its standard sets. One reason is they need to fit in the system, but the other is that hard tooling molds for production is quite expensive.

How come for a theme like BIONICLE they are able to introduce sometimes over a dozen new parts in just one set?
Bionicle sets don't actually make as many new pieces as they did. 

Typically, new pieces are weapons or heads, and LEGO company is already cool with green-lighting those. (They're sorta important.)

Gen 1 Bionicles did, admittedly, have a lot of new pieces, but Gen 2 sets, you will frequently find, try to recycle concepts and pieces, just in different colors or with different printing as much as possible.

Hero Factory was pretty revolutionary, with pieces that connected to themselves, (ball and socket,) but for that those were made, you'll see them incredibly often as staples of new sets. That particular kind of new-piece binge shouldn't happen again for a long time, if ever.

I don't know about a dozen pieces in one set though. You'll often find that "new" pieces are just old ones recolored, reprinted, or recycled.