Oh gosh, here I go with my story again. For those of you who've heard it before, look away lest you be bored to pieces.
Stacie, my 2nd F2 was the same way. He is very cat oriented but not very people oriented. I had to work very very hard to get him to accept me. I first had him quarantined in our master bathroom and I slept in the bath tub for a few weeks. Then I moved him into the office and slept on the floor for another few weeks. I was treating him for giardia and coccidia and he hated being given the meds. Our first 6 months together were very rocky and I was covered in spit from all the hissing. If looks could kill I'd be long dead because he was (and still is) the master of giving me the stink eye.
To get him used to being touched, I would play with him with a feather wand which he loves and I'd run the wand over his back and sides and from time to time I'd sneak in a pet or two. He started associating me with fun and things gradually got easier.
Also, I hand fed him a lot when he was a kitten as another bonding trick. I'd sit quietly on the floor with the food in my hand. After a week of this, I started gently petting him while he was eating. Another association with something positive.
One thing that I'm sure hampered our progress was my attitude. I was afraid of him because he bit and scratched me pretty badly the first night he was here. I know he felt my nervousness and fear and that put us both into a bad cycle. Then after a while I got mad because it seemed he hated me so much and I was trying so hard to at the very least put us on a level of mutual respect. Well, he picked up on the anger and away we went into another frustrating cycle.
So I had a long talk with myself, calmed down, and basically accepted that he would never be as big a part of the human family as our other savannahs. And that's when he decided that maybe I was ok after all. As long as I respect his boundaries and pet him when he's in an accepting state all is well. He has started giving me love eyes which surprised me so much I cried. He will follow me around the house and supervise everything I do and I had to learn that this was one of his ways of showing me that he thinks I'm ok.
One other thing, from your avatar I'd guess that he gets along with your other cat. But, there may be subtle territory issues going on there that could be a factor in his behavior. If your vet has given him a clean bill of health, perhaps he just isn't feeling secure in his environment and the challenge will be to identify what is making him feel that way.
Don't give up. If your guy turns out to be the independent sort, it doesn't mean he hates you, it just means he's independent. My guy is 2 yrs old and he is still making progress so I have high hopes that our relationship will continue to improve.
I always love your stories, Deborah!