They can still follow the history of Mary and Francis and play with storylines along the way. That is what the majority of shows and films do. This is the CW. If they wanted a show to be completely accurate, it would be on the History Channel.
The CW is made for drama and you can bet we will see a ton of it.
I like all the characters so far and even though I favor MF, I also would like to see a little of MB. They are making it harder for me to believe that MB can happen though. I felt similarly with Elena and Stefan in TVD. They were the "epic love" that no one could break up and BAM she is completely "in love" with Damon. IDK... that sort of thing bugs me and I am starting to see it happen in Reign.
I am still a little confused about the flashbacks in the first episodes. Did little Mary play with little Bash as a child? I feel like we need more insight into Bash's past and his childhood relationship with Mary because I was under the impression from the pilot that the two of them were close. I watched it a while back, so my memory could be failing me.
Also, is it considered a spoiler to talk about M&F historically?