Well... I never watched any machinima beyond Freeman's Mind, but I think I know how you feel based on my experience with other forms of medium that are not machinima.
I think the main problem is that many machinima/SFM creators are mainly animators, not writers. And many amateur writers have a nasty habit of thinking that melodrama is the only kind of drama. (Also being incredibly tone deaf)
Fun fact that is kind of related to the topic: Hunt Down the Freeman was going to be just one of those "serious" machinimas. (and I think it should have stayed that way)