First of all, quite a few of your examples - like Lily leaving you and Shawn's death - were some of the few things that had to happen in the game because they tied into the story of the comics.
Secondly, in pretty much every game that has ever taken player choice into account, it's always been the ending where we really see the consequences of our actions. We've just passed the halfway point here, we don't know how all of our choices turn out yet.
Thirdly, we do have to temper our expectations here somewhat. It's not reasonable to want the game to become drastically different in story halfway through just because of your actions. You can't expect to have your episode 4 take place in Chicago with all different characters while mine takes place in Savannah. At the end of the day, Telltale does not have infinite resources and can't possibly make a game that has such large variations. How it all ends may end up being drastically different, but the lead up to it, by necessity, has to be pretty similar.