Why do HiSeq4000 run types cost more than the runs on the HS2000 and MiSeq?

The reagents cost more, the flowcells cost more, and overall they cost more to operate. On the other hand if you build a good library, you'll get a lot more data! The price PER BASE is actually cheaper. As with the other instruments the number of good reads is determined by the length of the library (length is figured into how many clusters can be seeded), how tightly the library is sized, and the content and quality of the library.