The Kaiju that appear in SSSS.GRIDMAN are combinations of those from the original Denkou Choujin Gridman and any Kaiju (sometimes Ultra) from an Ultra Series. Considering how Akane had a lot of Ultra Kaiju sculpts stored in her display case, its not a huge stretch for her to use any of them as a reference.
In a way, it is somewhat of a deconstruction of the Isekai genre as Akane left reality to spend her time in a world where she's perfect, all powerful, and everybody who meets her loves her. But being in that world was terrible for her as it made her unwilling to go back to reality where she's not perfect or beloved. It was only when she mustered up the strength to wake up and go back to the real world did all the problems start to get fixed.
It's also a reference to Gridman's role as Yume no Hero (Hero of your dreams, his theme song), as he helps Akane to wake up from a nightmare of her own making. In his original series he once entered people's dreams to save them from a Monster Clown army created by Khan Digifer, so it's something he has already done once before.
Yuta Hibiki being given the motif of G1 Cliffjumper may seem off until the plot comes in full circle: G1 Cliffjumper is a Fish out of Water in the world of Transformers: Shattered Glass where Autobots are evil and Decepticons are heroes, just like Yuta losing his memory in a place he supposed to be familiar with.
With the reveal of Yuta's true 'amnesiac" nature as Gridman's splintered half, the role of G1 Cliffjumper goes to Gridman himself, the real immigrant to Akane's Tsutsujidai. Like almost everybody else in his class, Yuta is also part of the Shattered Glass gijinka, with his being the SG Cliffjumper, whose dead before the G1 counterpart arrives.
Why does Transformers and Super Robots gets referenced a lot? Because Takara was the sponsor of Denkou Choujin Gridman and the references may be how Tsuburaya try to send in their thanks for playing a major part in founding Gridman.
Also, since the cyberspace is essentially Akane's dream, every reference would be the doings of her subconscious.
Akane creates Devadadan to kill her homeroom teacher because he didn't apologize for bumping into her, yet kills Sakiru and her group even if she apologized. However, from episode 1 itself, Akane and another classmate's words imply that this isn't the first time Sakiru played volleyball in their class, making Akane's anger a bit more understandable.
Suddenly it all makes sense as to why Gridman resides in Junk and materializes in the city instead of cyberspace: Because the entire Tsutsujidai IS a cyberspace.
Given how Gridman typically fights in a technicolor citylike landscape, Akane must have put a new coat of paint on a portion of cyberspace to help keep the illusion. This is confirmed in episode 11 when we see her in an "unpainted" part of town.
In that case, boys invent great hero might have been a brief preview. After Takeshi gets his own Acceptor, the first area he fights in as the new Gridman is the middle of town.
The reason for Tsuburaya to disallow director Amemiya into adapting Ultraman into an anime: well its not really that hard to imagine, but since the Ultraman manga is about to have one in 2019, they might try to prevent two Ultramen anime from different studios from competing with each other.
Akane seats at the back of the class and her left faces the window, which is basically the setting of almost every anime protagonist that take place in high school. In a world where she is a god, Akane saw herself as the protagonist despite being the other way round.
Why couldn't Gridman and all the Assist Weapons be all together in episode 4 yet are able to fully combine in episode 8. It is because Junk couldn't process their full-size data the first time but could their minimal output.
In-Universe: In episode 10, Akane learns that Gridman is in Junk, which is in a thrift store. Since thrift stores are where people get rid of things they don't want, she understands why Gridman's been hard to find.
In episode 9 Yuta is the only one who sees Gridman, and always in reflective surfaces. Gridman wasn't trying to get Yuta's attention, Gridman/Yuta was seeing his own reflection.
Anosillus the 2nd's choice of music (The piano version of "Yume no Hero" used on her ancestor in the original series) working on Yuta to wake him up makes a lot of sense when it's revealed that He's the original Gridman. Hearing the old tune was easily enough to 'wake' him up.
Kaiju stink. Anti being given a bath to deal with this foreshadows his moving beyond being a kaiju. Likewise Akane repeatedly calling him a failure. A kaiju that fails to be a kaiju is an Anti-kaiju. In other words, a hero.
Rikka representing Akane's IRL self is foreshadowed many times. Akane treats Anti to an extravagant buffet as a reward for epically defeating a mighty enemy; Rikka gives him a simple meal out of kindness. Akane leaves him out in the rain; Rikka gives him a bath. Akane sends a kaiju to hunt down Arcadia because she wants nothing to do with them; Rikka politely turns them down. Where Akane performs exaggerated, grandiose gestures, Rikka eventually does the down to Earth, simple equivalent for the same person.
Related to this, Rikka representing Akane's 'real' self makes the whole show an object lesson for Akane. Her idealized self is an admired but unhappy loner. Her 'real' self is part of a superhero team, has a cool boyfriend, and is friends with a guy who gets her kaiju otakuness. Taken all together, it's subtle message from herself to herself that her 'real' self doesn't need a perfect world to be happy.
Not to mention, the girl who wakes up in the live action section of the finale is heavily implied to be the real Akane. Take a close look at her, and you can see she resembles Rikka far more than the animated Akane. She doesn't have Akane's cropped, white hair, but long black hair like Rikka. You can even spot Rikka's signature cream-colored jacket hanging in her room.
Look at the difference between Rikka and Akane's rooms. Rikka's room is extremely detailed and full of the items you'd expect to see in a regular high school girl's room, almost as if it were lifted straight from a memory, which would make sense if Rikka is based off the real Akane. In contrast, Akane's "dream" mansion is completely empty and devoid of detail, signifying that even with the larger house, she doesn't know what to actually do with it other than just possessing the house itself since it's something she doesn't have in the real world.
Despite being blue, Rikka's eyes have pink highlights, just like Akane's.
The relationship between Akane and discarded garbage/junk. She uses kaiju to rid her perfect world of garbage she doesn't like, yet her room, filled with the kaiju models she loves and presumably created for cleaning her perfect world, is filled with garbage bags. As much as she says there are things she wants to be rid of, she still keeps the 'garbage' in the same room as her beloved kaiju, implying even if she says she's discarding them, she still values them enough to keep them by her side.
The heroes operate out of a Junk shop, implied to be more of Akane's cast offs. Yet she keeps it right next to her house. Rikka is in the same house, yet is her best friend, and represents her real self, even if they've drifted apart. The computer used to channel her powers is even called Junk, and yet is instrumental in saving her, even against her will. Anti, constantly referred to as Akane's failed creation, is the one who dives into the most powerful terrible monster of Akane herself in his weak human form to literally drag her out of her own hell, and can be considered her personal Gridman Knight in shining armor, but with a kaiju aesthetic she'd prefer to Gridman's own Ultra (kaiju destroying) sensibilities. The very things she tries to discard all come together to save her because they are good parts of herself.
Akane claims that Rikka was created so that she would always love her. But actually, that's backwards: since Rikka is based on the IRL Akane, and the Akane in the anime is the escapist fantasy that IRL Akane created, anime Akane is created to be 100% lovable by Rikka.
In the end, Anti stays in Akane's perfect world. As her creation, he was a kaiju created into an Anti-Gridman, before evolving into a being who is Gridman's equal. He's taken the place of the Venora as a kaiju who maintains her perfect world, and who better to do the job than Akane's personal Gridman? Akane Agent Gridknight!
That Gridman is the same one from the 1993 show was foreshadowed by his Initial Fighter form, the Assist Weapons, and Junk. Rather than being nostalgia grabs, their appearance and abilities were influenced by Gridman's memories of the first show when he was attacked and split up. Considering how Akane's world is the same as the real world, Gridman may have been nostalgic long enough to get blindsided.
In a way, Yuta really did fall in love with Akane like everybody else. But unlike everybody else, Yuta fell for the real Akane, who Rikka was based off of.
Akane killing people with Kaiju for extremely petty reasons makes more sense when you realize she's the only real human there. Would you feel any guilt erasing bits of data you thought was trash data? Especially when you have somebody whispering in your ear to give into your worst traits? That you're a God and you can do whatever you want?
Gridman appearing before Akane in the opening. He's not there to stop her villainy, he's there to save her from Alexis!
Gridman being supportive towards Yuta's feelings for Rikka makes sense with the reveal of him being the original 93 hero. He was observant towards the behavior of his previous human allies, Naoto, Yuka and Ippei and how they had their love lives (Naoto with Yuka, while Ippei was unlucky enough to have multiple rejections), thus uses his experience to help the boy with his feelings.
Once Gridman regains his original tokusatsu form, he is vastly more powerful than he was in the first show; it Alexis wasn't immortal, the final battle would've been a Curb-Stomp Battle. He healed up during the show, regaining his original strength, which was augmented when he fused with Anti and the Assist weapons to regain his true form. Alternatively, he just simply trained between shows so he wasn't reliant on Powered Armor and Humongous Mecha.
Gridman shows he's not only superior to the Kaijus Akane makes to defeat him but also to the background Kaiju who repair the city after every fight. Having a heart that can empathize with other's pain, Gridman's Fixer Beam doesn't only fix Akane's world, transforming it into a near perfect replica of Earth, but also mends Akane's heart to give the young woman the strength to go back to reality.
In the final episode Rikka (Akane's perception of IRL Akane) realizes that Yuta likes her and not the fantasy Akane. Given that Yuta is probably based on Akane's IRL crush, this is a major epiphany.
Why do characters from Akane's world feel and act like realistic people while people from the real world (like the Neon Genesis Junior High School students, Gridman, etc.) feel more anime and tropey? Well, since Akane is sick of the real world, she could've wished for a more normal life! One that looks like an anime, of course.
Notice how Yuta is the only character from Akane's world with Shonen Hair (apart from herself). If the theory that Akane has a crush on IRL Yuta is true, then she probably gave Yuta Shonen Hair so that he'd be easy to spot. Also, because she likes anime. While Rikka and Utsumi don't really have Shonen Hair, their hairstyles are very distinct from the background characters. The Fridge Brilliance doubles with the reveal that Akane wanted to be friends with all of them, so she probably intended for her and them to be a Four-Man Band.
Akane is said by many to be the ace of her class and the most beautiful student. Is this trait legitimate or just a part of the setting in a world where she is a goddess?
Mix of that and Online avatar being nigh-impossibly attractive. But even then this isn't perfect as not everyone bows to her and Yuta falls for Rikka instead.
The monster in episode 5 is so big that it even camouflages itself as the mountains. So how many casualties are there in the monster's own hide when it gets penetrated by Buster Grid Beam?
Fortunately as revealed later on, Akane created the entire countryside for the sole purpose of the field trip, so everything just gets erased after that. But would that mean everyone who lived there also gets erased as well?
As early as the first episode, Akane shows an interest in Yuta. Rikka was this close to getting kaiju'd due to the fact the boy Akane might like might like someone else instead
Super unlikely given later developments; as messed up as she is, Akane is as invested in Rikka just as much as Yuta, if not moreso - the nature of their relationship just makes things a little weird.
More of Fridge Tearjerker but its implied Yuta was created to be Akanes perfect boyfriend but rather than falling in love with Akane, he fell for Rikka who was likely based off the real Akane. It certainly wouldnt be good for Akanes already shattered self-esteem when it appears the boy she created specifically to fall for her instead fell for her real self.
While not as horrifying as the other entries, it is either unnerving or funny to consider the Les Yay between Akane and Rikka and knowing that the real Akane looks more like Rikka, resulting in the idea that the ship is essentially Screw Yourself.