I note that most of the comments I've seen have been written by people who saw 12 Monkeys first and then chose somehow to see La Jetee.
Comparisons are useless beyond the basic feel of the story.
When I first saw 12 Monkeys I didn't know its relationship to La Jetee, a film I had not seen in 25 years. Yet, I recognized this relationship almost immediately, even though I could not remember the name of the movie. This I realized through the feel of the story ... down to the very end.
In many ways the short film was much more stimulating ... even though I had forgotten the name of the film I had never forgotten the images or the impressions it made upon me. I guess that's strange, but as I recall I saw it at Rice University as a part of a film festival back in the 60s.
Granted, films must sustain themselves somewhat through the years to maintain their value as true art, but one must always remember the context of the film's original audience.
I wonder now if the dependence on stills to portray the story had any influence on Ken Burns? Heh ... he's made a reputation on the same technique.
My point ... accept both movies on their own merits.