Biggest problem that I had is that it eventually becomes a challenge to manage the framerate. I realize there are ways to fix this that are intertwined with the gameplay, but I'd rather play the game instead of butchering kittens and other things in an effort to keep the game performant.
Second issue is with military organization. I never really became confident in my ability to get the squads doing what I wanted them to do (wearing the proper uniforms, training with a crossbow).
Despite this, I've had a lot of fun with the game. Building, farming, and managing a metal industry is a lot of fun. The barrier to entry is still pretty high, and I don't think the announced additions are going to change that.
(haven't played in the last year or two, so my criticism may be outdated)