Have any of you considered that this may have been a negotiating tactic? Whether to pump up their value to Nintendo, or to some other interested party (publisher or purchaser), it's in SK's best interest to drum up a supportive reaction. Not to mention that said prospective backer may have wanted proof of SK's worth, since their sales figures and productivity obviously aren't spectacular. Thus, a show of fan base coupled with high reviews for games are where SK's value lies.
As for the disagreement, I'd bet I know where that lies, too. Denis and crew probably wanted to go in certain mature directions with Too Human or some other title that Nintendo, though willing to let others publish, is still not comfortable putting its relatively family friendly brand upon. That's right, if Dyack wanted to explore sexual themes in ED2 or TH, I don't think Nintendo would want their name on it directly. Blasphemous/controversial religious content may supplement that as well (more doubtful, considering ED).
If this is true, then I think that Nintendo is making a mistake. Instead of trying to keep the Nintendo brand holy, Nintendo should be making a "sub-brand." The readiest analogy that comes to my mind is Disney (kid friendly parent company) and Touchstone (mature content owned by Disney).
Now that I think about it, that, too, may have been the point of contention. Nintendo may have wanted to "expand" SK's brand for use by other Nintendo publishing houses, rather than attempting to build one from scratch (ignoring the obvious choice of the wholly owned brand "Retro Studios" for a moment). Perhaps some deal where SK publishes the work in name. SK, protective of its name, refuses, and their ways part somewhat. This option seems a little more far fetched, though.
We'll see, though.
BlackGriffen