Eventually Dr. Jones will start feeling unhappy and isolated because he wants to be with others of his kind but all other supermutants he's met are mindless and agressive. Also mostly everyone in the wasteland fears and distrusts him because of who he is.
If the PC joins the Institute he will decide that he wants to conduct some scientific research into restoring intelligence to other supermutants. He'll ask the player to help him set up a lab and get information about FEV and other things that will help his research. When he and PC have gathered what he needs to get started he'll begin his research and will give the PC an additional science based bonus.
If the PC joins BoS, Dr. Jones will hear from someone in the Brotherhood about supermutants who retained their intelligence, maybe on the West Coast or in the Mojave, maybe somewhere closer and will want to go there immediately. PC can talk him out of it but he'll then want to set up an expedition to go there and will ask PC to help him find others who want to go there, get weapons, provisions and everything needed for such a journey. After finding some people who want to go with Dr. Jones the quest is completed and the player gets some kind of exploration based bonus, but the journey is delayed until all the necessary preparations have been made (until the end of the game).
Finally the PC can persuade him that he'll never find any company he can belong to and he's better off sticking with the PC. This will get Dr. Jones some kind of combat bonus, because travelling with the PC involves a lot of fighting.

After some travelling together will open up about his past. When he was young raiders killed everyone but him in his settlement, including his whole family. Hevily traumatised, he escaped and found his way to another settlement but all he could think about was revenge on the raiders. Eventually he tracked down the gang that attacked his settlement and methodically hunted down everyone in that gang. His revenge complete, he realised he didn't really have anything else he cared about in life so he just wondered the Wasteland tempting death. You can tell him that in the Wasteland this is as good a way to live as any and he will get a further combat bonus. Alternatively you can help him find things and people to care about, it will take time and he will be reluctant at first but your efforts will be successful eventually and he will get some kind of noncombat bonus (maybe crafting?) and will no longer complain if you leave him at the base.

She will keep asking the PC about their pre-war life and what it was like and will refuse to believe anything negative you tell her about that time. She will tell the PC how much she wished she lived at that time instead of now. You can then tell her that that time is gone and will never return, she will then become even more paranoid and defensive of everything else in the Wasteland but will get some bonuses towards defending the PC in combat, something like increased combat strength if PC's health is low. Alternatively you can restore a house for her at your home base to something close to a pre-war condition and get all kinds of pre-war stuff to create a piece of pre-war life for her. She will then become happer and calmer but also more detached from the post-apocalyptic reality, her mind increasingly in the past as she imagines it. Not sure what sort of bonus this would give.