Windreader Sphinx, Gravitational Shift, and Radiant, Archangel are some powerful flying themed cards that you may have overlooked.

What would you suggest swapping for them?

Pongify: There are better options if you really need the effect.
Battle Mastery: Setting yourself up for a 2 for 1 for an effect thats only ok
Favorable Winds: Crusade isn't a powerful enough effect for edh
Devastation Tide: for a land. you need more.

Definitely making some swaps! Pongify has been useful, what are the better options for a one drop removal spell for me?

True Conviction ends games

I prefer Path to Exile over Pongify

True Conviction is too expensive and is countered every time I've attempted to play it in games. Path to Exile might actually be a better choice. Gaining a land might be better than a token, although I could just bounce the token.

Rapid Hybridization is pretty much the same as Pongify too I believe. I still think they're good removal if you decide to run more removal.

I know it's about the same. Just feels weird cutting it. Playtesting will show which is best lol. Thanks for the input!

Glasses of Urza guarantees you will always get a card into your hand every turn.

I like the idea, but what would you swap out for it?

I'd honestly swap out Judge's Familiar. Sure it can counter certain spells, but most people can afford the extra mana. It's so easily planned around unlike a normal counterspell

Judge's Familiar had actually saved the game multiple times. I've found that people usually tend to look at untapped lands when thinking about counters

Telepathy is fun. You might also benefit from Aboshan, Cephalid Emperor just tap down their non fliers on their turn so you don't get hit. Also it nicely sets up your Sunblast Angel. Magus of the Moat unless you can pull for an actual Moat. Sphinx Ambassador is kinda high cost, but it is a super sweet finisher.Bident of Thassa or Coastal Piracy could also be pretty nice.

Telepathy actually draws a ton of hate, which is why it came out. Although having no way to fetch Magus of the Moat sucks, it seems like a good fit. Same with Bident of Thassa. What would you suggest swapping for them?

Maybe Unexpectedly Absent and Divine Reckoning

Archangel of Thune and Baneslayer Angel are two very efficient flyers that would work well with this deck. I also think Drogskol Reaver could find a place in here, since card advantage is always nice. I'm also a huge fan of Grand Abolisher for preventing people from interfering with my plans and Grand Arbiter Augustin IV for making those plans come to fruition faster. I also highly recommend finding room somewhere in your mana base for Arcane Lighthouse since it is absolutely bonkers. And finally, if you can find room for it, few things can beat a turn 0 Leyline of Anticipation for a Blue player.

What would you suggest swapping for Arcane Lighthouse? Everything else you named draws a lot of instant hate in my playgroup. I really appreciate the suggestions!

I'd cut an Evolving Wilds personally, since color fixing isn't that hard in a two color deck. And have you considered running Tamiyo, the Moon Sage for additional control?

I have considered using Tamiyo, the Moon Sage, but it would be for her first ability. I can cover that with Yosei, the Morning Star and Lyev Skyknight, which are both tutorable

Telepathy, Gitaxian Probe, could help with the hand thing

Telepathy was in the deck, it just drew immediate hate. Gitaxian Probe is only a one-off, which limits it's usability

As far as your description goes, I think you have enough creatures. The benefit of a toolbox deck is that you can run less creatures since you can tutor for them. Now it comes down to whiff creatures you run. For example, as good as Yosei, the Morning Star is,I don't know how good he'd be in the deck. He works much better when you can reanimate hill turn after turn. If you did want to make him work, (and in general) Karmic Guide is good to have. Then you could get a high market and you would get more value from him.

Yosei, the Morning Star is actually an all star in the deck. He taps down problem permanents, usually keeping them down. I've had mixed feelings about Karmic Guide. I know what it can do, it just hadn't performed for me. Although I am looking to swap out akroma, which is just too expensive

Drift of Phantasms seems perfect for this deck. Fetch it up with Isperia then use it to tutor for any number of helpful things (Rhystic Study, Fireshrieker, etc.). I have a similar deck that is nowhere near as tuned for competitive play, but you still might find a few good ideas: http://tappedout.net/mtg-decks/spy-drone-armada/