To be honest, I really can't stand the boatload of history stuff in this story. So most of the time I just skip it
But for me, the one thing I REALLY have an issue with is the Protagonist. Though maybe that's because a heavy bias on my part and I compare him too much with Suguha while Ken is only a regular human (bar the power) that didn't know the future.
Hijikata 2 Ending Spoiler
I do have to say though, after all the stuff that's going on in the VN, The Hijikata Ending 2 is realllly satisfying
And Spoiler again for Hiji Ending 2