hey barium,
I wanted to give you some advice, and i hope you dont take this the wrong way. First let me say, i am by no means a professional remixer, so I wont give too much advice on the actual mechanics of that. I am still learning myself in that regard.
At the earlier part of this thread, i recall you mentioning that you were fairly new to remixing. That being said, it seems to me that this may be too ambitious a project to take on at this point in time. Often, it is hard enough to remix 1 song let alone multiple ones. With one song, you have the capability to concentrate on a set of melodies and rhythms that you can work with, which makes for a much easier project. With this song, it seems that the different themes kind of run into each other.
Honestly, that is going to be natural since more thought is going into how to make the different songs mesh than how the entire song as a musical thesis sounds as a whole. To begin with, trying to collaborate themes is a tricky business, since they have to naturally flow as they exist, or you could have a big mess on your hands. I have a hard enough time trying to make 1 theme work let alone 2 or more. Im not saying youre not capable, i am just suggesting that it may be too ambitious a task at this point in time. Basically, if it were me, i would shelve the whole project until i felt i had the capability to do it.
Im sure you feel capable, especially after working your ass off on 13 different versions ( believe me, thats exactly how many versions i have into my latest mix), but maybe try working on another project for a while that is simpler, and less challenging, so that maybe once you have successfully mastered 1 (granted i dont know if you have or not), maybe you will have a better time trying to remix many.
About the piece itself, i think dynamics need to be considered. The piece will come alive if you really take into consideration crescendo and decrescendo. Also, attack would be another thing to think about. With the orchestral instruments, (especially brass), nothing is worse than having mushy attacks trying to re-enforce rhythm. If you can pick from samples with more attack, i would definitely do so. Also, there are many musical textures that make a short appearance and are gone for the rest of the piece. This will detract from the unification of the song as a final product. Using the same instrument textures throughout the piece on different themes would help create a more seamless segue.
I would also reconsider some of the textures you are using. That synth-ish trumpet that appears about halfway through the piece doesnt fit the mood or style of the piece IMO. Consider the melody structure as well. MAbe dont completely give the entire melody out right away. Reserve it, and give it out in hints here and there. Do so throughout the entire piece. Dont just say, ok this part is gonna be chrono trigger and this will be mario... Make them apart of each other in a way that is recognizable.
Hope that helps