I liked season one better simply because it was much more thrilling, a missing Will who we barely see or hear of, nobody believing Joyce at the start putting you the viewer in a frustrated state since you can tell she isn't lying, and Eleven being under the constant threat of being recaptured. A whole more mystery vibe which was thrilling to say the least.
That being said, season 2 was epic in it's own rights, especially since it brought into play a more frightening antagonist in the mind flayer