My interpretation of it was that Pokemon Sun has a normal day and night cycle, but Pokemon Moon is reversed. Offsetting it by 12 hours means that if you play Pokemon Moon in the day, it will be night in game, but if you play during the night, it will be day in game. A person with Sun might want to trade a day exclusive Pokemon for the night exclusive Pokemon of a friend playing Moon, since it's too much hassle for them to try getting other Pokemon late at night.
I'm sure we will still have version exclusive things, but this sounds more to me like we will have a ton of stuff exclusive to certain times (like Pokemon which only appear or evolve at certain times of day), which will be easier to get in certain versions depending on when you have time to play. For example, a Pokemon which can only be found late at night will probably be hard for most people to get in Pokemon Sun without messing with the 3DS clock. Meanwhile, anybody playing Pokemon Moon would be able to get it easily, since the night in game takes place during the real life day.
I would expect to see more of the same kinds of things we've seen before in terms of day-night exclusivity. We will have Pokemon exclusive to the day and night, like how Ledyba and Spinarak are in Johto games. I would also expect Pokemon which only evolve at certain times of day like we got in X/Y. The fact that the times are different in the two games add an interesting twist to this.
I think this is a pretty cool idea, though I was planning on getting Moon and I'm not too sure if I want it to be night all the time when I play.