I think they were both pretty terrible.
Last Stand tried to cram too many characters and too many plot ideas into one movie without doing anyone or anything any justice. It completely failed to deliver the Phoenix plotline even though the two previous movies had been carefull building up to it, it wasted time introducing new characters who ended up serving no greater purpose in the movie, and it gave such letdown endings to many of the central characters from the previous movies (mainly Cyclops, Rogue, Mystique, Jean, Xavier... oh hell - everyone, really). Overall, it was one big hot mess of a film that clearly lacked dignity and direction, and it was such a sad way to (temporarily) end a pretty good movie franchise.
Wolverine: Origins was a boring and forgettable gun show with explosions and ineffective fanservice. It was drawing from source material that could have easily been made into an exciting film, but it pretty much ruined it in delivery by speeding through the most interesting revelations of the original comic version of the Origins plotline within the first five minutes of the movie, and the spending the rest of the time retelling the story that was already mostly uncovered in the previous movies, tripping on plotholes, and marching in cameos of characters who really deserved more screen time that the script warranted them (what a waste of a good Gambit). It just basically ruined any chance it had to be engaging by killing all suspension in the very beginning and by focusing on telling the story the movie-going audience already knew, and not even being fun while at it.
I can't tell which I disliked more. Both movies bored me to tears between the occasional facepalms.