First of all I have to clear the air here, I am talking about the traditional jujutsu, not BJJ, we are indeed completely different. Jujutsu was the art used by samurai centuries ago to fight in the war when they were stripped from their katana. Judo branched out from jujutsu years ago in modern Japan. That's the history of it.

In the fighting system, what I understand is, Judo improvise their techniques from Jujutsu and became an art based majority on throwing and joint locks. Judo gradually becomes a sport since then, although there are still traditional schools in Japan that teach traditional Judo, but sadly a lot of Judo schools train Judo as a sport today rather than as a martial art. Jujutsu kept a lot of deadly and lethal techniques in our syllabus. Those techniques are forbidden now because they kill and we do not simply kill ppl nowadays isn't it? So if you ask me what's the difference, I would say Jujutsu has more techniques other than throwing or locks, and the way we throw are different from Judo. The style of throwing, position of body, something like that.

I am not here to make a comparison by saying Jujutsu is better than Judo or what, I would say in fact they moved on to a different path. Every martial art is a good art, it depends on how well you understand your own art.