It seems to be the consensus all over the internet that The Matrix is better than Matrix: Reloaded. But I haven't seen any really good reason why. The Matrix has the advantage of being first, thus it is unique and original. Hell, it was mind-blowing. The Matrix: Reloaded - been there, done that.
But Matrix: Reloaded contained some interesting concepts, not just the Agent Smith "virus" either. It tells us that good requires evil, and vice versa.