Naruto SOSP 4* is better than either of those two, but if you really want Minato or Shisui for some reason, I'm going to go against what everyone else said here and say Minato is better, even without his bond skill barrier. I'm saying this not only in terms of the current meta (Naruto SOSP) but what we will be facing in the future, Obito [10 tails Jinchuriki] BT. Basically, you need to think about how Minato and Shisui match up against these two threats.

Against SOSP, neither of them are great honestly. Shisui theoretically might be a little better since his mystery and standard are undodgeable and for Minato it's only his mystery. However what really screws them both over is that they are heavily reliant on their chase to scale and to reset their mystery cooldown, and BT Naruto has like a 70-75% chance to dodge chases. If Shisui's chase does hit him it's great since it's irremovable ignition (goes through debuff immunity) which is really nice at countering Naruto's own healing. But again it's very unlikely you'll be able to do that chase, unless you get some support ninja like NY Tobirama to run alongside Shisui (NY Tobirama can decrease evasion rates), and he isn't cheap either. As someone who has used full BT Kimono Shisui against SOSP BT, I can honestly say...it's hard to win. It's hard with Minato too but I've seen it done.

Going into the future terms of fighting Jin Obito, while I don't think either of them are perfect counters, Minato seems like he'd be better. Obito is immune to pure ninjutsu damage, which is what Shisui's standard attack is, as well as the offensive attribute that he scales on. Shisui's standard and chase 2 (the combo chase) also do secondary fire attribute ninjutsu dmg which I think does affect Obito since it's elemental, but I'm not entirely sure how this is calculated in terms of damage he takes. But on top of that, Obito also causes the Ninjutsu Sealing debuff to attackers, which means Shisui's ninjutsu scaling will be disabled and his ninjutsu will be reduced by 50%. The only good thing about Shisui in this scenario is again his irremovable ignition, which counters Obito's healing. But because he can't scale and his ninjutsu will be reduced, he probably won't be able to do much other damage to Obito.

Minato on the other hand scales his attack and combo rate. His standard attack is pure taijutsu damage, which only takes into account the atk stat. He can a|so decrease the opponent's defense when they hit him, so the more Obito hits him the more Minato's attacks will do. As far as I understand, Ninjutsu Sealing only stops ninjutsu scaling, not all scaling, so Minato will still scale even under this status. Unlike Naruto SOSP, Obito doesn't dodge and he doesn't have super armor so refreshing Minato's cooldown shouldn't be the issue. If you're able to outspeed your opponent you might win.

Even outside of these matchup considerations, I just think Minato is more versatile. Shisui doesn't have many support skills but Minato has some. His passive that gives ignition, tag, and the defense drop (or enfeeble/weaken if you use the Y bt) is a great defensive passive skill. His ability to revive can a|so be used in a support capability, especially if you have his barrier but even if not.

Ultimately it's up to you, I've written out what I think are the pros/cons here but I'll add a few more for your consideration if it helps you decide:

- Shisui can chase off his own mystery and standard (repulse to low float), Minato can't chase off his own attacks. Neither of them are great in 1v1s where it's only the position 1s left standing but in this situation Shisui is better, because his standard is undodgeable and he can chase off his own attacks.

- Shisui's true debuff immunity (reflection) is great but it isn't going to protect against irremovable debuffs, like Ninjutsu Seal (Obito), Hiraishin Mark (NY Tobirama), or irremovable ignition and paralysis (Rinnesasuke, Indra, himself). And irremovable debuffs just seem like they're becoming more common.

- In my experience Shisui is pretty squishy (he dies fast). He has one dodge but he can easily be combo'd down. Minato can dodge standards which helps him survive longer. Not that it matters vs Obito or SOSP Naruto since their standards are undodgeable, but it still helps to be able to dodge the supporting ninja's attacks.

Lol sorry this was long, anyway hope it helps you, even if you disagree with me.