I think the idea of Nintendo doing a game to cover the Seal War is a major stretch. For one, at this stage in the series, the Seal War is not that spectacular of an event nor is it really important anymore. It might have been kind of a big deal when it was first mentioned in A Link to the Past, but I don't think Nintendo has any serious attention on it as far as the plot goes. There's also the theory (which I support) that Ocarina of Time is the Seal War. There's plenty of evidence to back it up, and just conceptually it's kind of weird that Nintendo would make ALttP and mention this Seal War, this origin story for Ganon, and then make Ocarina of Time almost right after (minus the side-story, LA) that covers... oh, guess what? Ganondorf's origin. Both involve him seeking the Triforce. Both involve him getting sealed in the Sacred Realm.
While there are most certainly problems connecting the two, especially now, how can you look at what Ocarina of Time's story contains in the context of when it came out and not say it was intended to be the Seal War? It seems exceedingly obvious to me.
If Nintendo is going to make a new game that covers a war - which would be a drastically different setting; not a bad idea in itself - I think a better choice would be the Unifying War. The one that predates Ocarina of Time. Unless of course Skyward Sword covers this somehow, which is probably kind of doubtful at this point. See if it was the Seal War, it would still be Ganon again, he would still be seeking the Triforce, he would probably still kidnap Zelda, all the classic stuff. But with the Unifying War, Nintendo could tell a much more unique storyline. Not that I want to knock Ganon or Zelda's tropes and standards, but doing a war-based game would already deviate from that, so why not go all-out?