The thing that annoyed me about The Matrix is that I didn't think it was nearly as clever as it clearly thought it is. It had a pervasive smell of intellectual smugness. I much prefer movies that present themselves as rollicking good fun, but include some nice little bits of brain-fodder.
I like The Matrix as a guilty pleasure: it's so fun listening to the pontificating. I haven't seen Dark City either - looks like I have a lot of watching ahead of me.
I liked Dark City a lot.