I definitely think that there will be a part two, but I don't know how. I'll tell you why I think so, though.
Although the ending was pretty emotional, I think it was too abrupt. I mean, up until Link reached Zant in person, he was pretty calm. When he finally met Link, it's like he hit his head and became a complete lunatic. I think this was Nintendo's way of shortening the game, as cheap as it is. I mean, there were very few mentions of Ganondorf before this point, which tells me that they originally weren't ready to introduce him yet. Cryzeu als unintentionally hinted on this when he described one of his drawings by saying how a lack of appearances made it difficult to draw him.
On top of that, I thought Hyrule castle was too short and simple to be the final dungeon. Sure, there were a lot challenging monsters (though I personally liked fighting the knuckles), but it was just short, especially compared to dungeons like lakebed temple, temple of time, and arbiter's grounds.
And did anyone notice that Midna's secrets were being revealed little by little, until Gerudo Desert, when she practically told everything at once?
I might be overthinking, I don't know, but that's what I saw. What do you guys think?