Mobius to Mobius 1, the player character from Ace Combat 04. He even uses the same callsign. There are also Talisman and Shamrock, the two leading protagonists of Ace Combat 6. Finally, Sky Eye. The two latter characters even mention (though it is not explicitly stated) the respective wars they took part in: The Usean Continental War and Operation "Katina" (Mobius and Sky Eye) and the Anean Continental War (Shamrock and Talisman).
Also, the EAF logo is modeled after the ISAF logo.
This line from Rainbow Dash at the end of chapter 8:
Rainbow Dash: (to Fluttershy) Donít worry about me. Weíll return... and weíll take back our shattered skies.
In chapter 15, there is a flashback moment taken directly from Ace Combat 6, only that Shamrock tells Talisman about his dead little sister rather than wife and daughter, like it was done in the original.
Chapter 18 has Lightning Bolt reading a book about four pegasi ponies who fought in a conflict together and disappeared after said conflict ended. The book's title? The Unsung War.
Gale says almost the same thing that Crux does at the beginning of mission "End of Deception", just replace Aurellia with Equestria:
Gale: To all units. This is probably our final sortie. Unlike you, fighting on the frontlines, I sit behind the monitor and observe the battle. Iím in no position to ask you anything, but please allow me this one request. End this war and return to Equestria. That is all.
Black Star says a couple of lines that may immediately bring up an image of Ilya Pasternak:
Black Star: Everyone fights for what they believe in. For me, there is only one thing left worth fighting for in this world. And that is the future. Only by fighting you I can let my sins take reign.
When Rainbow Dash comforts Fluttershy in chapter 10, she briefly paraphrases Solid Snake.
Rainbow Dash: You may not believe me, but I understand how you feel. Every pony feels horrible when they do something awful for the first time, especially if they kill someone. Unfortunately, killing is one of those things that become easier to bear the more you do it. During the war, all of ponykindís worst instincts may surface. Itís important to not let them take you over.