That was by design. Some episodes focused on the prosecution story, and some on the defence.

If you cast your mind back, you'll recall a long sequence (almost a whole episode) where they tried to recreate the drive from the library to the Best Buy, thus poking holes in Syed's claim that he couldn't have travelled that distance in that time. You can't say, based on that (and other episodes that were pro-prosecution) that the series was pro-prosecution. I thought it still finished with a lot of doubt on both sides.

Well, they sort of showed early on that the prosecutions theory was wrong. But that doesn't mean he wasn't guilty. And when presenting his story, they spent considerably time debating wether it was true or not. It seemed pretty balanced to me.

It's not the media's job to give equal time to "both sides" on an issue or be "balanced." I trust Serial, based on the exhaustive reporting of their first story, will do a fine job exploring this story.

I think that was the thesis of that season - what was the nature of the evidence used to convict someone to life in prison.