I think it ended with the last episode mainly because it ran out of steam. There simply wasn't another story to tell about Bowe or other aspects.
I also think that Bowe is once again in the sights of the military because he told his story to Serial and to the other interviewer. Knowing what a big deal Serial Season 1 was, the military recoiled at Bowe's story being out there and analyzed by so many listeners. In the end, I don't think that happened, but the military assumed it would.
The difference I see in this season and last is S1 seemed like a serial telling of a story and S2 seemed like long form journalism. I liked the exploration of Bowe's ordeal. I gained a lot of knowledge of how things worked from the inside out. It had its rewards for listening through the series. I came out thinking Bowe, though guilty, is being scapegoated. He possibly deserves some sort of punishment from the military but not prison time. (I'm not informed enough to know what else the military could do to punish him other than prison.)