There are a couple of differences. First of all the Pro 2 has different filters, which basically give you both the character of the Prophet-6 combined with that of the OB-6, albeit the circuits are not 100% identical. But ultimately, you get a different sound. Then you get the 12 additional super waves which are nice for thickening things up especially in paraphonic mode. Talking about the paraphonic mode: that enables you to do stuff that is impossible on typical poly synths as you can select different waveforms for each paraphonic voice. This provides you with a more experimental type of polyphony if you like.
Then of course you get the fulsome sequencer and all the additional connectivity, be it one extra MIDI out (MIDI Out 2/Thru), CV ins and outs, and the audio input. This makes the Pro 2 a perfect candidate for controlling other gear, especially now that you can send out CV trigger and MIDI CC automations via the sequencer and the according outputs respectively.
And finally, the Pro 2 is sort of the peak of all modulation monsters in the Sequential portfolio with its 51 mod sources and 180 mod destinations (including the 4 CV outs and 64 sequencer specific MIDI CC destinations) that can be used in a mod matrix consisting of 16 freely assignable and 25 fixed mod slots.