During the ending of Skyward Sword it is revealed that Demise is responsible for all of the monsters and evil things that torment the land. He is then sealed and/or killed with the Master Sword, which is then thrust into some pedestal. This much is clear.
In The Minish Cap we learn that all the monsters of the world are sealed inside the Bound Chest, which was sealed by the Hero of Men by thrusting a sword into it. When this seal breaks, monsters return to the land.
What we have here is a strong connection between the two games. The only flaw in this plan is the blades involved. In SS, the Master Sword is used to seal Demise. In TMC, it is the Picori Blade. However, the Blade looks identical to the Master Sword, so that makes things a little easier.
I like this as a strong connective to confirm that TMC comes immediately after SS. The releasing of the monsters is a pretty direct reference, and on top of that, if Ganon is to be the second coming of Demise or his spirit re-embodied or whatever, he has to be let out somehow before OoT. Thus, the first three games could look something like: SS - TMC - OoT.
But I have more evidence other than just monsters. TMC blatently refers to Sky People, and does so ever-so-casually. By the time of TP, the sky people are a myth, but in TMC, Link heads up to the sky and chats with these people like it's no big deal. This leads me to believe that the people from Skyloft that settled in Hyrule still regularly visited the sky to the point where it did not become a legend yet; that is, the sky people's existence wasn't shrouded by the same mystery as TP yet. This fact, combined with the release of monsters, suggests that TMC can directly follow SS.
Finally, Zelda is known to protect or contain the Light Force, which is EASILY relatable to the power of Hylia. This connection is clear. Now it's not part of my theory but I think it's a nice touch that Vaati looks and acts similarly to Ghirahim. So what we can see here is that Vaati aka Ghirahim2.0 is out to break the seal of his master at the begining of the game to release the monsters and obtain the Light Force. I think when you piece this together, it is very clear that Minish Cap should follow Skyward Sword directly.
So that's my theory, I'd like you guys to go ahead and poke holes in this now, if you would please.
Edited by D~N, 10 December 2011 - 07:53 PM.