I think SovereignKage got it right. Kabuto is powerful, but Minato is better. And if we are counting Yin Kyuubi for Minato, that not only gives him great increases in all ways, but it would be difficult to lock him into any genjutsus, as proven by fellow jinchuriki Killer B.
I feel like if the Tobi vs. Minato fight had never happened, everyone would be like "Minato is speedy but you can't hurt what you can't touch Tobi has Kamui and Tobi has Sharingan Minato doesn't Tobi wins". But Minato is super smart and strong. He caught a TBB with a FTG Barrier, evaded capture by Kamui, and within minutes created a strategy that brought him victory.
The same would happen here. Kabuto won't be a walk in the park for him, but Minato wins.
All the people giving Minato the victory are talking only about his accomplishments as a ninja along with the variant of him having Yin-Kurama (which isn't the case, since Minato didn't have Kurama in his living form, as stated by the TS), but fail to mention how exactly Minato would be able to defeat Kabuto. As I already said, both Rasengan and kunai slash aren't going to work on the latter, even while combined with the FTG. And no, I don't think that the Big Ball Rasengan can finish him off either, while Minato isn't even known as a BBR user, the only thing he used was a somewhat larger regular Rasengan which didn't kill Tobi as far as I remember. The only thing I see virtually working on Kabuto is the Reaper Death Seal, but it automatically leads to a double KO.
Edit: And besides, regarding the genuis, actually, it was Kabuto who was said a) to rival Kakashi's level and b) have the skills superior to those of Tsunade in her prime, while both these statements referred only to his Part 1 form which didn't even have any of his later enhancements. So, it's not like Kabuto himself cannot be hyped the same way as Minato, even by the accomplishments, though I'd rather avoid it, since hype isn't really the appropriate way to decide the outcome of the fight.
Minato cant escape the sound genjutsu,it required itachi and sasuke to break it.
Kabuto can stay in Sage Mode as long as he pleases. Also Minato has no way of escaping or counter White Rage or Sound Genjutsu, and stabbing Kabuto with a Kunai will do Jack shit to him, same with a Rasengan impact as he will just heal the damage just like Oro would.
If Minato tags him then Kabuto can be sended to the ocean (war arc when Minato arrives and saves the alliance from the juubi TBB)
Itachi and Sasuke got hit by white rage and could still cast genjutsu on each other to get free, Minato can likely use FTG to get out of danger and undo the genjutsu
If for some reason Minato can't close in the distance to mark Kabuto then he can summon Gamabunta connecting the frog to Kabuto and using chakra link for the teleportation (like he did in his fight aganist Kurama)
If you give a bunch of edo tensei to Kabuto Minato could still win if the contract seal he used on Obito works also for the edo contract
EDIT: That was Tayuya genjutsu, I confused the two, but the thing should still work
Idk how far Kabuto's regen goes, but I do remember Minato setting up some techs to use on Obito that looked like a near simultaneous all-angle assault.
In any case, I think a lot of this fight depends on knowledge. If there's knowledge, then Minato will try to BFR him quick before Kabuto can get the Sound Genjutsu off. Even with SM, I think if anyone could actually tag Kabuto, it'd be Minato.
But if Kabuto gets Sound Genjutsu off, Minato is kind of screwed. The two Uchiha couldn't get out of it on their own. So Minato almost certainly couldn't.
Minato could also try some sort of sealing. He's rather good at sealing, but we haven't seen many techniques from him so to say he could seal off any of Kabuto's techniques is a real stretch.
So yeah, I think Kabuto would win. Honestly mainly due to Sound Genjutsu. Without the Sound Genjutsu, It'd be so much more even and I'd be more inclined to say Minato finds a way to bring Kabuto down after a long hard fight. But as it stands now, seems like Kabuto would inevitably win.
@Squinty
Fair point, but do you think Tayuya genjutsu is somehow amped in the hands of Kabuto?
Like Shikamaru could break himself free thanks to his shadow
Seems like it immolizes you but you can still use chakra, if that's true Minato has some ways out of it
Still, a good strategy for Kabuto could be spamming it (I don't know why he didn't do it actually)