Like many others, I found the end of the season last night very underwhelming and rushed. I wondered how it could possibly be that they didn't have a more concrete ending for the season, and it was all such a big asspull.
Then I remembered the "tacked on two."
Let's roll back the clock. Discovery was originally supposed to end the season at 13 episodes. On May 17th, 2017, it was announced that the first season was being expanded to 15 episodes. We don't know for certain what those episodes were, but we do know that filming of the season didn't wrap up until late October.
I had earlier hypotheses about what the "tacked on two" might have been. One was that the prologue was originally shot in part or in total as flashback, but later stretched into a full two-parter. Another was that Magic to Make the Sanest Man go Mad was one of the tacked on ones, because (aside from some Burnham/Tyler romance) it was pretty self-contained and not critical to the show. Some have suggested it was Si Vis Pacem, Para Bellum, but I find that unlikely, given the Klingon arc from that episode transitions cleanly into the mid-season finale.
Considering the 13th episode ends with a cliffhanger - as if it was meant to be the season-ending show, I am left with the conclusion that maybe that was meant to be the end of the season, with the Klingon War finishing up in the second season (meaning they didn't fully know how they were going to close out the arc yet). Only someone high up in CBS realized, before the show even aired, the redesigned Klingons weren't working out (and maybe Burnham wasn't either) and basically commanded Berg & Harbets to wrap up all of the Season 1 arcs in two additional episodes, so they could start with a clean slate and do a more conventional Trek show in the second season.
Thoughts?