As mentioned, theres a massive amount of filler. Almost all of the second episode could have been cut without much bearing on the story but because theyve got to make the required episode count and have at least one budget-saving episode, we get almost an entire episode of Gwen and Jack on a plane being rendered. Admittedly, part of the episode is the discussion of how the worlds medical system needs to be completely reformed because of the Miracle but that could have easily been shifted into a more streamlined second episode beginning with the rendition flight landing in America.
As well as this, we get two episodes spent investigating the Overflow Camps (camps set up to treat and/or destroy people that overstretched medical facilities cant handle) which, other than featuring recurring character Vera Juarezs death and revealing what happens to peole that have been designated Category One (people who are braindead but physically cant die are incinerated), has no effect on the rest of the story. After two episodes spent infiltrating the Camp, in which the only significant thing that happens is Vera dying, were told about massive public outrage over the Camps but dont really see it (which breaks the golden rule of show, dont tell) but nobody does anything about it after the purpose of the camps are revealed to the public which makes the whole thing a bit redundant.
Episode Seven could have been massively stripped down as well. Cut the subplot of Jack and Italian immigrant Angelos relationship (which went nowhere and made the episode feel a bit like Queer As Folk meets The X Files) and instead have a much shorter flashback in which Jack gets seriously injured in a fight and then heals which someone sees and thinks hes the devil, thus leading into the plot of him being held prisoner, killed repeatedly, and his blood being harvested and sold. Plus it would have much more of an impact on Jack to come face to face with his captor and repeated murderer on their deathbed in the present than him seeing an ex-lover in the same situation. After all, theres got to be quite a few of those scattered around time and space.
Also, were only told about the destruction of blood banks in Buenos Aires and Shanghai (facilities that were controlled by the Three Families (the people behind the Miracle) and held stocks of Jacks blood) that took place immediately after the Miracle in episode nine. Once again were told not shown and its only slotted in a few lines of dialogue right when its relevant, with no foreshadowing whatsoever.
Like I said though, there were just far too many episodes (five would have been perfect) and to meet that episode count there was just way too stuff much shoehorned in there that was either too drawn out or not developed enough. Which leads me to the next issue...