Well, I could offer my explanation for those things... Just remember that Aonuma is talking pretty generally here. It should be obvious by actually playing the games what exactly happened.
But several parts of that don't make sense. He didn't just "do something outrageous", he went to war with Hyrule.
Yeah, Aonuma doesn't specify the crime he is commited for, but as TP tells us, that's pretty much what he did. There is no contradiction here, however, as far as I can tell.
They didn't merely leave him alone
Didn't they? Aonuma says the execution scene takes place years after the ending of OoT, and until that time, that's pretty much exactly what they did.
and more than that, he didn't use the Gerudo as troops.
In TP, it is implied that he did (he was the leader of the gang of thieves that attempted to invade the Sacred Realm). In OoT, many of the Gerudo are his "followers." In short, I don't see the problem.
All the Sages are of an indeterminate race.
Yes, they are clearly different from the OoT Sages.
He didn't want to "obtain the power" - he already had it in the first place.
He wants the entire Triforce, you know.
If the scene of Ganondorf's execution takes place "several" years after Ocarina of Time, then the Skeleton Knight would have to be Ocarina of Time Link.
Well, we can't say for sure the Hero's Spirit actually fought Ganondorf, but sure, it's implied.
It doesn't solve the problem of Ganondorf dying with no clear way to be resurrected, either, unless he doesn't actually die in the ending of Twilight Princess.
He was reincarnated in FSA, you know. In that sense, his death sets up his return in the IW perfectly.
I can accept that it is supposed to take place in that timeline, but it is still a retelling of that story - it's not the same tale, not exactly. Too many facts change between the two of them.
Yes, I agree with that.
