TOO MANY REVELATIONS!@!!!!
Around the same time Ryuuken shows up to save Ishida and offer him a way of getting his Quincy power back, Isshin shows up in Shinigami gear to save Kon (in Ichigo's body) from an arankaru. Grand Fisher, no less. There was a general collective reaction of "...WHAT" from most people, and from Kon, because there really wasn't anything to suggest that Isshin was anything more than a normal human. Crazy theories have been thrown around in the fandom for a long time, so someone might have brought Isshin theories up before, but there wasn't much to back this up, aside from the fact that Kubo Tite has surprised us before, and that he doesn't leave his characters underdeveloped.
But yes, Ichigo's dorky dad is an extremely powerful Shinigami, and this is the first time he has been in his Shinigami form in twenty years. He took down Grand Fisher in one hit, without even releasing his zanpaktou. (I'm not the only one interested in his zanpaktou, right?) We don't know anything regarding his past life as a Shinigami, aside from some hints on his uniform and from a conversation with Urahara, who shows up after Grand Fisher is defeated.
It's quite possible that Isshin has been using one of the gigai that got Urahara banished from Soul Society. A gigai that drains the wearers reiatsu, is untraceable, and can reproduce? If that's the case, I can understand why Soul Society freaked out, especially if it'd mean more human children like Ichigo being born. Urahara mentions that it would be "problematic" if Isshin were to blame him if he had become weaker, so he obviously had something to do with it. Isshin was essentially a normal human for the last twenty years - he couldn't save his wife from a hollow, he couldn't even see ghosts. Just what happened to allow him to regain his powers is unknown, unless it was Ichigo's crazy reiatsu spreading like a disease. Again.
Despite the fact that it's only been twenty years since Isshin was in Shinigami form, he has been absent from Soul Society for much longer than that, otherwise Rukia would have recognised him. He must also have changed his name, or taken Masaki's name when living in the human world, as someone in Soul Society would have recognised the name from Ichigo. Also, when Ryuuken and Isshin met and the former calls him "Kurosaki", the latter is surprised, and comments that this is the first time Ryuuken has addressed him like that. While it's possible Ryuuken only referred to Isshin as "moron" or something similar beforehand, it might just be that he had a different name back in the day. Shiba, perhaps?
Captain of this ship
Shinigami!Isshin has something interesting wrapped around his arm: something that looks like the tattered remains of a captain's jacket. While we can't see the insignia that would identify the division, it does have the familiar diamond pattern along the bottom - like all the other Gotei 13 captains, and like Urahara (a previous captain). It's interesting to wonder of which division he could have been captain of.
The fourth
The current captain of the fourth division is Unohana Retsu, who appears to have been the Captain for a long time (all the longer standing captains have long sleeves; captains for a shorter period of time seem to have shorter ones on their jackets - they are more likely to battle?). She is a calm woman, and remains unruffled by most things that happen. The fourth division are the medic division, and our Isshin is a doctor. However, he seems too comfortable in battle to have been captain of this division - the fourth division are generally considered useless in a fight. Hanatarou, a seated member of the division, didn't even carry his zanpaktou around - he has no use for it.
The eleventh
Zaraki Kenpachi is the current captain of this division. The eleventh are battle hardened and somewhat bloodthirsty, and they are very loyal to their captain. Zaraki is unusual, both in the manner in which he became captain, and in that he is the only captain not to have achieved bankai. He is incredibly strong, and relies on this strength, and this strength alone in battle. He doesn't even know his zanpaktou's name.
Zaraki became captain after defeating the previous one in battle. Who this captain was is unknown. This battle would have taken place in front of at least 200 members of the division. Isshin is obviously powerful in battle, and could have been captain of this division. However, presumably, the previous captain must be killed? This hasn't been clarified, as far as I know, but if Isshin was defeated, Zaraki is not the type to leave him alive. Unless Isshin had some help with an escape in the form of Urahara. After all, there were 200 people watching.
Or something else?
With the current story arc, we've been hearing things about the royal family, who rule over Soul Society and exist in a separate dimension which can only be opened with the obviously named Royal Key. This royal family is protected by a royal guard, and so far we know next to nothing about them. Perhaps Isshin is part of that guard, although one would imagine the royal guard having a different uniform to a normal shinigami - even a captain, one more befitting of their job. When I hear the world royal, I imagine plumes. As it stands, I'd place my bets on Isshin being a former Gotei 13 captain, the uniform and jacket are too similar to what we've already seen. Plus, if Isshin was part of the royal guard, or another of Soul Society's forces, it is unlikely he would be in close contact with Urahara, unless there is some other conspiracy waiting to be revealed. And you just know Urahara had something to do with Isshin leaving in the first place. When in doubt, blame Urahara. The swine.
See: the title of this website