How old is he? Ten months?
-He never shows aggression. He has only hissed a few times, but only out of fear. (like when his paws get caught on something and I have to help him)
That's a good sign. In time he'll likely stop hissing altogether. Within the few year or two of getting my six month old feral kitten (avatar pic cat) he stopped hissing completely, when he's scared now (around strangers) he just cowers... he has no fight in him!
-He tolerates being held, but would prefer not to be. He tends to just freeze up in a ball if held and his claws do come out, which might mean he is fearful, but unless you were to handle him very quickly or aggressively he won't make a fuss and will just go with it. Could he ever develop into a lap cat?
He could become a lap cat, but sometimes cats like this never become a lap cat and would rather sit beside you or around you. Heck, some cats even if they weren't feral are like this, it depends on the cat. My cat (banner pic cat) was a semi-feral cat (used to be owned by someone as she was spayed) and now she is a little lap cat. When I'm at the computer she sleeps on me and she also sleeps on me at night. It took a lot of repeated attempts, not just to get her used to sitting on my lap, but to get her used to laying on me on my bed. At first she'd freeze up and jump off right away but slowly she came to realise that sitting on my lap=scratches! And that laying on me on my bed wasn't so bad, either. Of course, before this step I first had to get her used to enjoying being scratched. She doesn't sit with anyone else in the house (even though she's completely relaxed and friendly towards them), I suppose this is because I tamed her so she's "my cat".
-He takes to my wife much more than me. I think this is because she gives him his space and doesn't make much eye contact with him. I tend to pick up up and give him a treat now and then and I notice what he's doing a lot more. (can you tell I'm a dog person?) Should I always let him entirely make the first move? Like never actually approaching him?
I think a lot of cats take better to women. I'm not sure exactly why, but that's been my experience. I would say definitely let him do the decision making. Do not pick him up if he does not want it; my aunt tries this with my once semi-feral, the cat has always hated her for her inconsiderate approach. You need to let these cats accept you on their terms. To this end, try sitting close to him on the floor, slowly move your hand towards him - if he looks like he's going on bolt, stop, and only try moving it closer when he relaxes. Keep your voice low around him, try and walk around the house quietly, things like that. Just make sure you don't "manhandle" him and tower over him, that doesn't get you anywhere. it will take time for him to trust you but if you do the things I's suggested he should eventually come around.
-He gets very, very hyper and playful, but if you get too close to him while excited he bolts away from you. (which is odd because when he is sleepy/chill I can walk right up to him with no problem.)
Well, I wouldn't worry too much about this... in time this behaviour will likely change.
-While I'm not his favourite, he does give me affection when the mood is right. He also has a very strange habit of taking my spot on the couch when I walk away for a few minutes. When I return to my spot he usually stays for a minute and leaves. What's up with this?
It's hard to say. Maybe he just likes the warmth, heh.
-Also, he never enters our bedroom. He roams the rest of the apartment, but the only time he goes in there is while we are sleeping. If I ever enter the room while he is in there, he dashes out.
Are there loud noises in there, or anything that he may not like? Is there no way out of that room besides one door? He might feel trapped in there.
I'm just wondering if I should be expecting him to develop more socially or if this is how he will always be. I am willing to just leave him alone if there is nothing more I can do. Is there?
I'd say take it slowly, and he could and should continue changing in personality for the better. My feral kitten took over a year before he'd walk close to the door leaving the apartment (he didn't like the people outside!) and even at two or three years of age, we were still noticing changes in his behaviour for the better -- he became the most loving purring lap cat. The same goes for my semi-feral, we were noticing changes years after she was "tamed", like meowing when she'd enter a room, or walking right up to me when I'd be standing outside. It took over two or three years before she's allow me to scratch her tummy -- before that despite looking like she wanted me to, without warning she's bite, hiss and kick and scratch at me... I know, silly me for continuing to try! But I've noticed over the years somewhere along the time she lets me scratch her there without caring in the slightest. These things happen slowly, and you might not even notice them as they happen, but one day you might find yourself going "he never used to do that!"...