It looks ok to me too. I see that one pillar in your upper window thingy is clipped into the other wood, and that looks better when done with stone but a lot of wood clipping is unattractive. The devs let you clip one thing into another and its a huge help most of the time (like trying to make rounded stuff without gaps), but once in a while you get an ugly.

You will get used to it, if you like the graphics of the game. I think the devs were partly going for a 'made with crude tools' for basic wood and stone structures, or at least in part. Later things with higher tier tools look smoother, better put together, but its a shame that the advanced wood doesn't have wall & floor tiles (yet?). I suppose you have fine wood now, as I see core wood there... look at a fine wood table, for example, it looks sanded and smooth.