Images and/or cutscene images of Ciel, Zero, and the resistance can be found in Prairie's room, along with Alouette's old clothes. Her room is also filled with cyber elf plushies.
Prairie's stuffed animal is the same one that she (Allouette) has had since Zero 1.
Hyleg Ourobuckle from Mega Man Zero 2 is sticking slightly out of a tree in Area A-2 (Forest) in the Giga Aspis boss fight section. Apparently, some of the snake platform is embedded in the trees as well.
A Pantheon is looming out of the underground area's background in Area C-1 (City).
An E-Tank is just sitting on a crate in the same background. Coincidentally, in the game, you can purchase E tanks from Cedre in the engine room, and obtain W cans by hitting the doll in Prairies room.
The Crane Game section at the Amusement Park (Area H-2) has stuffed dolls of various Cyber Elves, 4 guardians, a few bosses such as the pantheon core as well as Mayl and viruses from the Battle Network series. Characters can be seen as the cranes pick them out of the piles, in the piles themselves, and even in the background.
The Rush Roadster and Red Striker cars from Battle & Chase are in the city. Also interesting to note is the fact that the two boys who own the cars are wearing clothes (with colors) astoundingly similar to Nintendo's Mario and Luigi.
Aztec Falcon is apparently in the background along with the carousel in Area H.
The vending machines scattered throughout the city are designed like big E-Tanks.
Monitors in several areas of the city show the words "News Capcom." Capcom, of course, is obviously the gaming company, and could possibly be a reference to the "Capcom Times" newspaper from Mega Man 6 and 7.
Childre Inarabita from Mega Man Zero 3 hanging upside down in Area F-3 (Lake).
Area D (Highway) is astoundingly similar to the highway intro stage in X1, right down to the crumbling platforms and the fly helicopters braking the highway as they fall (Beecopters in X1). The music that plays is also a re arrange of the intro highway music.
The core of the Guardian Base is the same energy design that Ciel was working on in the Zero series.
The operators in the Guardian Base's command room look similar to the operators in the Zero series.
The theme that plays when Model W awakens is a re arranged version of "Fate" the theme of Dr. Weil. In fact, the beggining part loops for the Boss entrances, so as to not continue onto the melody itself. "Babel Tower" is also a re arrange of Fate.
In the city area, you can pick up bread from a lady's who's grandfather learned how to bake bread from an old Reploid (Old man Andrew from the MMZ series)
the reporter on the roof of the building in the city area says he want to be like the "famous journalist from the wars" which is a reference to Neige from Zero 4, although in the localization, the reporter is referred to as a "He" whereas in the Japanese version, gender is not specified
Vent resembles Mega Man Trigger from the Legends series. this could be simply coincidence, but there are also instances of the stitch mouths and the single red eye design appearing on places such as Model W cores, and on Serpents Final form.
Fleuve bears a striking resemblance to Perroquiet from the Zero series.
Omega Zero from Zero 3 can be found and fought in area N-1 following area M. The black hole background also has a flickering transparent image of the room Omega was originally fought in. (abandoned Lab with Fusion Omega debris) After defeating him, you can find a "Mysterious Stone" biometal, which upon beating the game, Fleuve allows you to use Model Ox, whose appearance is an exact duplicate of Omega Zero, and uses Ground pound moves from the X series. (The ones from X2, X4, and X6).
By putting either Zero 3 or 4 in the GBA slot in the DS, you can fight their bosses in area N, as an alternate way of earning model Ox.
In the above mentioned rematches, for the Z3 bosses, (the Eight Gentle Judges,) while using HX you can see their humanoid forms on the Biometal screen.
Each BM combo has a charge shot similar to an attack in X1, HX charge + ^ is Storm Tornado, FX has charged Fire Wave, LX has charged shotgun Ice and PX charge + ^ has charged Rolling Shield.
In Flammole's Area, as a mid boss, you have to fight the Lava Demon, which is an obvious Devil series reference (1, 3, X5, Z1, Z2 etc.)
The Data servers in Protectos' boss room are the same kind that Ganesheriff's body was made of in Zero 1.
The floating flames produced by Serpent's meteor attack resemble the Neo Arcadia emblem from the Zero series.
Mega Man ZX Advent
Wire Sponge from Mega Man X2 can be partially seen in the background near the bottom of the Tower of Verdure. Rospark, the boss of this area, also has a similar move set to Wire Sponge.
In the Floating Ruins area, there is a side quest in which you find "artifacts." The artifacts are named Light Bulb, Pinwheel, L Tank, and Balancer.
The Light Bulb is shaped like the energy recovery item from Mega Man 1.
The Pinwheel is the Yashichi item found in many Capcom games. It notably appeared in Mega Man 1, in which it was only found in the final level and restored all life and weapon energy once obtained.
The Balancer is the Energy Balancer found in every Classic Series Mega Man game since Mega Man 6. It's function is to automatically refill the weapon with the least amount of energy if Mega Man obtains Weapon Energy while not using a special weapon. This feature has been automatic for the X and ZX series, which is referenced by girl you give the Balancer to.
The L Tank is essentially an upgraded E Tank from Mega Man 5. Also, you can purchase E tanks from Nick.
The Utoboros from Launch Octopus's stage in Mega Man X1 can be found in the Oil Field (which is hinted to be the same area dried-out over the centuries). This Mechaniloid is later added to the display shelf at the Hunter complex.
The Model Train is the train from Zero 2 (and apparently Zero 1).
The Comic Book Secret Disk references Rockman & Forte 2: Challenger from the Future.
The Model a (ancient) mini game is done in the style of the NES Mega Man games. The final fight with Albert is in a ship remarkably similar to Dr. Wily's UFO from Mega Man 4 and up. When defeated, Albert does Wily's "bow for forgiveness."
The "Legendary Hero" Secret Disk shows a picture of Mega Man from the notorious United States box art of Mega Man 1. The description humorously mocks this art style, explaining that "These Legendary Heroes look more like coalminers in colorful outfits."
Queenbee has a move list similar to every other bee-themed Mega Man boss, such as Blast Hornet and Hornet Man. Since Advent came out before Mega Man 9, it is possible that Queenbee is alluding directly to Blast Hornet.
Model Z seems to self sacrifice himself. It is possible that this is alluding to the several times Zero has risked himself for the sake of others, such as X1 and 5.
Model A is obviously based on Axl, even though the "A" in question stands for "Albert."
Buckfire might be a vague Flame Stag reference, as they are both fire-deer bosses.
The flying beetles in the Legion HQ area are remarkably similar to the flying beetles in X2, which could be ridden on to get to higher places.
The Crushpactor in the Quarry area functions like the bulldozing enemies in Armored Armadillo's stage in X1.
Bifrost may be a vague reference to Wheel Gator from X2, as he is reptilian and has a buzz-saw wheel that operates similarly to Wheel Gator's weapon.
The Sage Trinity are named after the three doctors of the Classic Series. Thomas Light, Mikhail Cossack, and Albert Wily. Albert's actions mirror his namesake, as Albert is the mastermind behind the "Game of Destiny."
In the Legion area, there are several platforms which can be ridden and can damage enemies. These look similar to the carts in Armored Armadillo's stage and function in the same way.
The Mechanical Tree Miniboss in the Waterfall Ruins is similar to Wood Man from Megaman 2. It uses leaf attacks similar to him.
After defeating Atlas, you have to smash a wall made of what the raider describes as being Ceratanium, The the same material used in Megaman Zero 4 to make chips.
During the obtain the plant for the room mini mission, one of the plants you can choose is the Poplan from Z4.
The secret model obtained by collecting all the medals, Model a, is based on the NES Megaman 8 bit sprite design, and like the original 3 NES Mega Man games, cannot fire charge shots, and slides instead of dashes.
Bifrost in ZX Advent is voiced by Jeff Manning. If you've ever heard of a little series called Super Smash Bros.., you'll know that he was the voice of the Narrator and Master Hand in the first game.
What Could Have Been: As elaborated in this article, the Japanese promotional trailer for ZX is not just for promoting the game, but as a pilot for a planned anime series. It's sadly never made, for reasons explained in the article.