Saki: It goes without saying that his feelings for her have never completely faded (reference: A, B) - but he's grown up.
Initially, he'd thought that what he heard in "Saki's reality" was just that. But as the investigation went on, things became more clear. What he was hearing wasn't her reality. Saki was dead, her shadow wouldn't be there either. These were all extensions of his own feelings... every last one, from her words in that shop to his own shadow. It didn't change things - sure, he knew she wasn't the biggest fan of him. His feelings didn't - and haven't - changed about that. He knows he annoyed her, he knows she was never really interested in him. But even still, she helped him through some very difficult times and for that, he will always have a special place in his heart. Yosuke still has lingering regrets though; one that he never got to tell her the extent of his feelings, and two that he never got to apologize for being such a pain in her ass. His intentions had been good, but he was certainly overzealous, much like a puppy.
Yosuke knows that it's entirely possible that Saki can show up in Johto one day - be it at some point before she died, or after. It's something he thinks about fairly frequently. There's a lingering feeling of guilt, because he's not sure whether or not he should want her there. He knows all too well that as quickly as people arrive, they disappear -- and that she would probably be angry and resentful to be there at all. But on the other hand, it would be a second opportunity at life for her. There's no intent for him to ever pursue anything but his apologies... but he sure as shit would still do anything he could to protect her this time around. Including massive ass-kicking of anyone who tried to mess with her. Of course, that's just a distant daydream of his, but an inescapable one, nonetheless.
Rise: She's been his most consistent crush, but his feelings about her complicated that it's just... difficult for him. He's had a crush on Rise when he only knew her as "Risette," and becoming friends with her via the Investigation Team only intensified it. But it wasn't until being in Johto that he really started to see things differently. Becoming closer with her out of circumstance -- consistently talking to her and being around her alone made him fall pretty damn hard for Rise. She's been there to listen to him through some of her tougher times - and she was the first to see through Yosuke's bullshit (read: his shadow) and help him break through his repressed feelings for Souji. She supported him when they needed to rescue Souji, and she was by his side when he completely overcame his shadow via one of the "nightmares" during the shedinja ordeal.
Not only that, but she's always been the one to listen and offer advice when it comes to Souji in general -- and even other matters. When there's something he can't go to Souji about, he knows he can rely on Rise. There is a deep sense of affection Yosuke has for her - possibly the sort of love that's even deeper than what he felt for Saki. There's not much more he wants to do than just pull her close and be with her. Instead, he settles for really harmless (and obvious/bad) flirting. But there are a few major things that discourage him from doing anything about it.
The first that he doesn't feel like she wants to lean on him much. He understands it ("I'm just a second banana, you know?"), but it's still disheartening that even when he can visibly see hurt in her eyes, she'll shake her head and try to change the subject. It's changed a bit as of late, their conversation about her going to Kanto with Athrun put a bit of a fresh perspective for it. But at the same token, he can tell that she doesn't see him that way. Though there's far less disdain, from body language alone -- it resembles Saki in a way, and from that he knows that pursuing things would only end up changing their dynamic in some way that he doesn't want. And then of course, is the final and most major problem...
Souji: Things have definitely changed in terms of Yosuke's feelings on Souji since arriving in Johto. Best friends? Yeah, of course. But they've slowly started to change, to meld into things Yosuke absolutely could not fathom. He didn't know why a cup of coffee was making him happy, why some of the silly things Souji did would piss him off, and just how grateful he was for the way he was taken care of after the Gyarados incident at the Centre. They've all been a slow build to the fact that his feelings run much, much deeper than being best friends. Facing his shadow during the 4th wall, his desperation and determination to save Souji, and then being forced to face that shadow (and this time, overcome it) really put things in perspective for Yosuke. But even having the inkling of the truth, it's still a difficult road.
It's taken him four months to come as far as he has - accepting that those feelings are there and that they're real. There's been a lot of denial - a lot of talking to Rise, spilling his guts to Merlin -- a lot of tears. A lot of sleepless nights. A lot of nights where he sits by the pool and rests his head on Hokuto the Ninetales and just... wonders. Sometimes it's how he got into this position, others it's wondering what would happen if he said something. He's lost count of the number of times he's nearly woken Souji up from a dead sleep, or approached him just to say "Hey, partner... can we talk?" But no matter how many times he tries, the words stick in his throat and he totally chickens out. Those nights are usually sleepless too. It consumes him. There's the side of him that truly believes he'll be rejected. That's most prevalent. And Yosuke can't bear the idea of messing up his friendship over this.
There's other things too, though. There's the fear of one of them disappearing. If there's one thing Yosuke isn't sure he'll be able to handle ever, it would be something going right, only to have Souji disappear and come back with no memories. Or if he were to leave. He's told Rise that he wouldn't leave Johto without all of them -- he intends to keep that, and while there is a degree of truth (despite uncertainties because it's Johto), a lot of it is knowing that Souji's been through it before. He's seen Yosuke come and go, and he doesn't want to put Souji through that again. Discovering the plush pikachu the previous Yosuke won for Souji put a lot of things in perspective; he can't help but wonder if that ties into his own feelings -- that all along, somewhere underneath all this terror, fear, uncertainty -- that the feelings really have been there all along and it's just taken some bizarre catalysts to make him realize it.
However, for as far as he's come, there are certain things he can't accept yet. As far as he can see things as of right now, the feelings are purely emotional. He will vehemently deny that it's anything else -- though he's found himself in a few compromising situations. A few occasions of wanting brush a piece of hair from his eyes, sit a bit closer than is natural -- but when it comes to basic affection; hugs, kisses -- and anything sexual, he can't consciously will up any sort of attraction. He's not sure what it is -- though anyone who would know may say it's a coping mechanism, a way to justify the fact that he's not sure he wants anything to come of it. The sexual attraction is there -- as when Souji fell on him and the friction was just right, there was almost an incident. A very. Awkward. Incident. And then of course, there are those dreams he has on the nights he does sleep...
All in all, it's very complicated. Yosuke's life is haaaard.