It's a tough choice, but I would have to go with the Flashpoint Paradox. Admittedly, Hal Jordan is my favourite character, and had a more central role in JLW, the story from TFP was much more engaging and better executed. The fight scenes were far more action packed (but went a bit too far at times), and each scene involving Barry and/or Zoom was beautifully animated.
On the plus side of JLW was that it did make me laugh, while TFP left me depressed, and JLW also had superior character designs, whereas the characters in TFP were far too bulky - Aquaman comes to mind.
Praise should also be given to TFP for moving the central focus away from either Bruce or Clark and onto Barry, however too many characters were introduced into the relatively short film, leaving little room for character development other than Barry and Thomas. JLW didn't suffer this problem as the story was tightly woven around only a handful of characters.
Overall, TFP wins my vote, but only narrowly not because it is a great animated film, but because it was, for me, better than JLW.