JL Season 2 was pretty much all wrapped up and was sitting on the shelf for months before CN even got around to airing it. Timm really never even planed on JLU but at the last hour CN decided to renew it but with the new half hour format. This is why some of the original creators on JL never worked on JLU. They had moved on to other WB shows.
Bruce Timm was smart enough to know that after all the B.S. CN pulled during season 1 of JL, and somewhat with season 2, that the creators didn't want to leave the show open at the end like they did with Batman Beyond so they wrote an episode that ended the series yet at the same left it open if they wanted to do more. That's also why they did the whole Epilogue episode. BB never got that closure that Timm wanted. Timm though did say that they would have done more episodes IF CN wanted them.
The other factor was "The Batman" show which CN loved. For some reason, CN felt 2 Batman shows were bad and competed with each other. How could too much Batman be bad?