From what I have read, S.T.A.L.K.E.R Clear Sky will closely resemble the original vision for S.T.A.L.K.E.R Oblivion Lost / Shadow of Chernobyl, boasting improved AI, A-Life and numerous visual / game play enhancements. S.T.A.L.K.E.R Clear Sky is set one year before the events of S.T.A.L.K.E.R Shadow of Chernobyl. Logic would dictate that you play them in some kind of chronological order. However, the difference in graphics and game play mechanics between Clear Sky and Shadow of Chernobyl may be noticeable and potentially harm your enjoyment of the latter.
I am currently playing Shadow of Chernobyl now that it has been patched. It's a great game and I'm having a lot of fun. The graphics are still impressive and a lot of the annoying bugs I experienced during my first attempt at playing the game have been fixed or are so infrequent I do not notice them. Personally, I'm going to finish Shadow of Chernobyl first before playing Clear Sky. Basically, I don’t want to play Clear Sky first and then be disappointed by Shadow of Chernobyl because it is missing the updated graphics and game play enhancements I enjoyed while playing Clear Sky.