Long list of thoughts, in card order of appearence:
4 Fractals seem a bit low, I think 5 Fractals are the most common number for Fractal based decks, so I'd either add one or take them out altogether and wait to salvage them if we can.
2 Arsenics seem a bit low too. I think we need at least 6, flying arsenics is a good deck, and although I think we will manage to salvage at least some Arsenics along the way, maybe taking out some other cards to make space for this one is a good idea.
For instance, I'd gladly take out the Flesh Spiders for that.
6 Graboids means we will have just one Graboid deck out at a time. As predictable as they might be, grabbows are still one of the best choices out there. Also, with the addition of UGs, they make for a great deck, imo. Maybe slower than most grabbows, but surely more reliable against all sorts of decks. Most grabbow counters will be destroyed by that, too.
6 Novas have the same issue. Plus, Nova is very versatile and can improve many decks, including most UG decks - which in my opinion are undervalued.
I don't think Catapults will be required. If we have them, we might use them, but Flying Titans works well even without them. If it is meant as a counter to RT... it might work, but I still think it's not a primary card.
5 Morning Stars are low. Also, I think taking some light pendulums would be good. The reason is that they may be used for flying morning stars (which, with Wings, is probably a strong counter to anything Entropy could throw against us except the decker). Flying Morning Stars may also be our best bet against Time - it's immune to Steal or Reverse Time, and Time/Darkness duo is one of the decks we'll have lots of trouble taking down. 3 Sanctuaries are low as well - they are really a strong card, if you think about it, not just as Discord counter, but as healing cards.
I don't think we'll need 6 RTs to start with. ANY team fighting us will pack RTs on at least 50% of their decks. We can pick them up as salvaging cards while we go on, I don't see the need to take them since we don't really have a use for them out of the bat.
6 water pillars AND 6 water pendulums make me think we're going a bit out of our way with toadfishes. As good as fishes and squids might be, they aren't really our best deck, are they?
Also, 5 Wings in a deck are sufficient, in my opinion, so taking 15 might be an idea. And might I ask why we have 12 Firefly Queens while we have just 3 Bonds and 4 Hopes? Are we going to make 2 FFQ decks without enough cards for them?
While at the same time, not taking Fireflys means we won't have access to them for the whole War (nobody else is picking them). I still think some good decks can come out of Fireflys.
Changes I would do to the Vault as it is now:
-4 Fractal (Fractal decks won't be our primary decks, while it will be key to some other teams. Salvageable.)
+6 Arsenics (Enough to make a deck, plus two to split into novabows)
-6 Flesh Spiders (I didn't really see a deck with these which surpasses our other spider deck)
-2 Catapults (as stated above)
-6 Reverse Time (as stated above)
-3 Wings (as stated above)
-6 Firefly Queen (I don't think we'll see the need for TWO firefly decks in a single round)
-2 Sky Blitzes (are we really going to need 12 of these? I don't think we'll use more than 3-4 per deck)
-6 Earthquake (I don't see the need to have these. They may be strong, but they are completely out of target)
+6 Nova (as stated above)
+6 Graboid (as stated above)
+3 Bond (not really necessary, but these are always nice to have, and 3 seem low)
+1 Morning Star (as stated above)
+3 Sanctuary (as stated above, one of our best decks needs these)
-6 Water Pillar (as stated above)
+6 Firefly (as stated above)
TOTAL CARDS: 460
From the ideas I stated above, we could take out easily 2 Arsenics, 2 Bonds and the 6 Fireflys. That means 10 free cards we could use in different ways. For instance, taking back Fractals if we deem it necessary, or taking more Morning Stars / Sanctuaries (which I would like as an idea).
Also, a question to the veterans: isn't it better to focus a bit more on our best decks, so that we can play more than one per round? Also, if we had to discard lots of cards from a deck, while also not having some to back them up, wouldn't we be left with half-decks which result in many useless cards?