I think there was a right and a wrong to killing off J.
First off. The right was that J was too evil for the standards of Pokemon. When it got to the point of her wanting to kill Ash you know the writers were begging for PG. No can do, they still want to aim at the younger audience. So since J was too hard, she just went poof.
On the wrong side. I agree J had a lot of potential as a character. She could have been her own Smash Bros character. She could have increased the complication of the plot. She would have been the REAL epitome of a Pokemon Villain. Killing her off was a complete waste. And now it looks like she'll never come back, and there's no evidence of her having survived.
I'm going to admit, killing off J was probably the worst mistake ever in the history of the anime.