Very interesting but here's a few tips
First off:
1. Excellent amount of anime references in both music and drawings...But really man, the music doesn't fit too much, I suggest you take only songs for opening and ending, musicals for the rest, And fix the timing, at least start with the song slowly fading in instead of just popping it out of nowhere, world map is best with plain music too
1.5- Oh and if it's not too much, next time you make a flight scene, don't use Evangelion music, it doesn't fit, and please use fade in if you can or a good timing from start to a good midpart of a song or music which can repeat without messing up the song too much, though that's kinda hard to do, oh and, don't forget some special sound effect if you can
2. fanservice, nice amount, don't go too overboard or too low on amount, you should probably add in secrets and such for fun
3. Graphics aren't that bad, specially in the characters, but some of them need a bit of work(such as world map not by much, but the airplane itself....ok, I guess the wings was enough)
4. betcha you can make a better tribute to anime, create an innovative plot/storyline, or create a comical one like this one, but please, instead of diversifying the music overly, just add in more content thank you
5. Hafta say though, this is original, very, so anyways, This was some Great work, hope to see a sequel or something, sorry for the long comment, remember, these are just suggestions, if you're overworking yourself, take a break and then get back to it when you're ready