Shisui's chakra is within his eye as Ao was able to see it
You must be registered for see links
. Minato is a sensory type and we seen sensors tell others by their chakra like Karin, Tobirama, SM/KM Naruto, Nagato and Madara so sensing Shisui's chakra should work the same. We haven't seen many of Minato's use of his sensory ability but it is comparable to Tobirama who used it to tell the difference in his enemies chakra. Minato's sensory ability would be even better in SM, Naruto was shown to be looking for Kakashi's chakra back in Pein arc
You must be registered for see links
.
Also knowing about KA breaks the genjutsu as it did with Mifune, he wasn't in it after Ao told everyone and it's not something that can be used many times a day
You must be registered for see links
. Minato would also sense his chakra being disrupted if he was put under KA plus he uses clones and if he did then it would be harder for Danzo to make use of KA since the clone or real one would snap the other out of it.
As for Izanagi, Minato is the fastest ninja, he wouldn't need to waste his chakra on it, just dash, slash and repeat. If he marks Danzo before Danzo activates Izanagi then it's over, constant barrage of attacks. Izanagi wouldn't take off the mark if Minato put it on Danzo before it was activate, it only affects what happens after it's activated. Minato has the better summon from what we see as well.
If Minato goes into SM then it's over. Minato was stated to be tied with number 1 spot with Hiruzen by Kishi for a reason (
You must be registered for see links
)