Wrath of Khan. While on the surface it was a simple enough movie on the surface, it was subtly deep on a lot of levels with the themes of getting old, rebirth, revenge impossible odds and death. Heck, Khan's own bookshelf on the Botany Bay foreshadowed this nicely.
The action sequences in ID were no doubt better, but 30 years later that's a given. The difference between the two movies is TWOK used the action sequences to enhance the movie, while ID used them pretty much to carry it.