On Issei:
I know, but I basically gave him the power to sense powers as Auras, balance in Rise, Trance, and Burst, and Cure. And remember, he actually starts popping up in the future once Rosetta Stone gets built up. If I give him Teleportation Marker, then I've got to balance it out Reikan somehow, maybe giving him Shinra Banshou (or the Buddhist equivalent)? If Issei is the one who has it, I can have his power to nullify an opponent's PSI by matching it.
On Neko:
Yeah, she has an ability like Chakrams, but it works like Rud Hahn's Feline Claws from Veritas (she is called Neko. It's only fitting.)
On Kane:
I was originally going for Kane, but that was before I had gotten a good feel for her character through F/HA. She's a lot more refined and straight-forward than I gave her credit for, while Yukika is basically a cute puppy. Plus, having the mousy one snaps means I can parallel her with Sacchan. There's something... beautiful about the thought of that.
Instead, I was going to have Kane gain TK and Trance on top of Retro-cognition and have her act as the second brains/voice of reason of the group for when Shinji starts slowly going insane and since she's less likely to sacrifice people. Of course, I'm not adverse to her gaining Usui's Anti-Psi wave powers as well.
On Shinji Personality:
I am going to take it a bit slower with Shinji though, leave it vague since I've got a few arcs to flesh it out and foreshadow how his perception has changed. An idea I had was instead of him simply having nightmares, he's actually gained an Extra Channel to being able to perceive what he defines as evil from being the Holy Grail and made to watch for so long and right now his normal society channel is repressing it. When they go to Psyren, the atmosphere gives them a channel to a common perspective of the terminal and their baseline PSI, but Issei and Shinji having a pre-existing channel got it bundled with that and thus strengthens them. (Issei could vaguely intuit someone's Aura like Rin or Ilya before and in the future its basically turned into him being able to identify someone's power and alignment on the scale).
This way their trips to the future strengthens the channel and they begin to be able to influence the world around them on a greater scale in the past. Like for right now, Shinji might intuit someone's desire to inflict evil (i.e he can tell on intuition when someone wants to murder him or inflict bodily harm), but after a few more trips the channel opens wider/get stronger and he begins to perceive them via color like Kiri Nanaya's Pure Eyes could or a miasma. At it's height, he basically understands all the evil's someone does, what they fear, etc.
Of course, the stronger the channel, the more it pushes out the channel he has for normal society, with Rin (this is later in the fic) telling him that either he'd become so use to it that he'd be numb to acts of evils, or he'd go mad, thus forcing him to decide whether or not to have Shirou stall it by stopping him from going to Psyren any further (Rule Breaker the contract) since that's strengthening the channel. It puts him in a position where he can choose whether or not helping the others in the future is worth the risk to his own life/sanity, giving him agency rather than him being forced to constantly go along with it.
NOTE: I'm not married to any of these ideas, and if I can't work out the logic for the Channels, I'll just keep it vague enough to leave it up to the reader's perspective.