I enjoy both but Unlimited would be my pick, as well. Half-hour episodes but it had a more serialized approach especially during the Cadmus arc. Plus it featured a bunch of new characters and while some were usually only minor players in the grand scheme of things, several others were put in the spotlight alongside the founding members of the League. Overall the show probably had a better balance which granted was also built on a few stories from the initial two seasons of Justice League.
Don't have a lot to comment on Justice League at the moment but I always thought it was cool how it basically had mostly hour long episodes. And there are not that many cartoons I can think of that have used that format, even less at the time the show was produced. Might try a topic about cartoons with similar formats on another board sometime soon, since it could get a bit off-topic.
In a way they mirrored the original Super Friends which also started with hour long episodes, then reduced to half hour stories (and it's a different continuity but you could count Justice League Action which reduced things even more, with 11 minutes long episodes).