Yes. It should be 3 hours long. Here's my list of reasons why:
1) If WB decides to allow JL to be released in the runtime, it'll show that they'll start having their DC movie slate becoming filmmaker driven.
2) JL has to resolve and address a lot of plot threads including some Geof Johns said JL would address like why Batman became a killer, how people now see Superman as a beacon to the world after his apparent death in BvS (because some feel the scene where people gather at Superman's monument is not enough to answer that question), and why Flash, Aquaman and Cyborg decide to get involved.
3) It has a lot more characters to give an appropriate amount of screen time (like maybe some backstory) to 3 heroes (Flash, Cyborg and Aquaman and maybe a Green Lantern) since they'll need character arcs and motivations for their appearance in JL, plus they won't be introduced in their own standalone movies yet, along with the fact that characters of their part of the DCEU (Mera, Vulko, Henry Allen, Deathstroke and Comissioner Gordon) will be introduced in this movie, too.
4) There also needs to time to handle certain things too, like the return of Superman, the history and mythology of the Mother Boxes and giving Stephenwolf an appropriate amount of screentime to make sure he gets some sympathy from audiences and isn't seen as another generic Marvel movie villain (exceptions being Loki, Zemo and Vulture).
So, that's why I think JL should b 3 hours along.
Also, I know ur gonna tell me 3 hour movies don't do well at the box office. Well, if I may play a devil's advocate on that, Avatar, Dark Knoght Rises, Tianic, Hobbit 1 and Lord of the Rings 3 were billion dollar films yet they were over 3 hours long. If JL can be good as some those movies on an entertaining kind of level, the 3 hour runtime shouldn't be an issue.