I have them both and I use them both. To make a long story short, if I had to choose personally, I probably think the Prophet-6 is a more modern, usable synth. The Jupiter shows it's age and with being one of the first Midi synths, it has its shortcoming. Mine is equipped with Europa, wich gives back some interesting functions though.
The Synths are fairly similar, little details are keeping them apart. The Jupiter is more of a classic and you have to treat it this way. It sounds great, in my opinion. Not fat like the American synths, but you don't need always fat. It fits well in a mix. The BP Filter is great and gives a very pleasant soundscape, as well does the filter resonance. You will get the squelchy sounds that Roland is known for. Two Oscillators that can be cross modulated and controlled by an Envelope. It is a great feature and works well with the sync together. The envelopes are fast, the modulation amounts for pitch and filter are immense, that can results in very drastic sounds. Pitch of Oscillators can go from 64' to 2', just what a great range. You will get 5 octaves, non velocity keyboard and a bender section with an additional LFO. Midi is very bare bone, except when you get Europa, that is a game changer.
The Prophet-6 is a great modern synth. The oscillators are on par with the one from the Jupiter, the filter is different. In addition to the LP filter you will get an independent HP filter, in serial with the LP. That is different from the Jupiter where you have to choose either or. The BP Filter on the Prophet-6 is unbalanced since the HP filter is 2pole and the LP 4 pole. Very difficult to make these nice sounding BP Filter sweeps that the Jupiter can do. The PolyMod section is the staple of the Prophet-5 and the Prophet-6 takes it further, by giving you an increased range as well as more functionality. You can control PWM, Pitch, Filter, Shape with OSC 2 and that into the audio range. For low range you won't be using the oscillator for audio anymore, so the 2nd LFO comes at a cost. However, Filter FM is great, something the JP6 cannot do. And besides differences in sound design, the Prophet-6 comes loaded with modern features, like better Midi with CC and velocity Envelopes, multi effect section, and the sequencer. You will easily integrate the synth into your studio. Also only 4 octave, the keyboard is velocity and aftertouch sensitive.
Anyway, there is no right or wrong. I have the Jupiter-6 in use for over 20 years. I love that thing. It is my MiniMoog, the holy grail synth if it comes to analog. Many will probably don't understand, but I love how it responds. The Prophet-6 I own for 3 years or so when they announced them. I like the Prophter-6 a lot too. I always wanted the PolyMod and this synth feels better to me than the Prophet-5 with the 5 voices only. In the studio, the P6 is easy to place, syncing capabilities are working fine. Sometimes I use the internal sequencer for getting started. The Prophet-6 is no frill synth. It just delivers. The Filter is really nice sounding and I am using a lot of the cross/filter modulation capabilities. It is nice to have a bunch of effects right there and that you can save them with the sound. That is a great feature. Not always needed, but nevertheless. I am also a big fan of velocity and there the P6 wins big. It allows for much more dynamic also the sequencer is recording the velocity in the steps. If you plan a little, you will get a very potent tool there.
So, classic or usable, modern synth. The P6 sounds a little cleaner, but that can be the age of my JP6. But otherwise you will be happy with either.
It has better Midi, effects, USB, etc. The P6 is a great synth, can do a lot due to the PolyMod, sounds great, has an independent HP filter with resonance. The Jupiter-6 is similar equipped, however, it doesn't different things. Instead of the independent HP Filter you have a nice BP Filter, Sync in both directions, and a second LFO in the bender section. Overall, the Prophet-6 can do more, since it has Filter FM, which is missing on the JP-6