*** Spoiler Alert***
Your early concept is a kind of "is this voice real?" or a "which of these two characters is mad". This concept is interesting enough by itself, but as events unfold, the boys head down different paths with Apollo scheming, and Joseph kind of ambling along. This makes Apollo the more interesting of the two (in terms of drama) if we shall liken Apollo to MacBeth (willing to murder to gain the throne) and Joseph to Hamlet (willing to spend Act II waltzing where Claudius and Ophelia think he should dance).
From this point, we enter a “neutral” phase where political machinations develop that will help bring about the ending, and new characters are introduced.
After this phase, Apollo goes back to plotting and signs of madness increase. To hide the signs from his political enemies, Apollo is willing to disfigure himself. Joseph gets into prison and starts a cult dedicated to a voice in his head.
Introduce Caligula who will steal the spotlight. Drop the descent into signs of madness, introduce battle chess. Caligula loses, the boys are friends, there is no madness, there is no cult and what cult there was is irrelevant. The End.
PS: A world got blown up that we never really met and everyone is sad about it.
Now here’s where I draw the connection to A Beautiful Mind. If you think about it, the story begin-middle-ending never loses track of the main character and stays on its theme. Mind you, it has an easier time because it marries its central theme and stays there.
I’m not eagerly turning the page to find out how well Darth Maul is doing in Star Wars. I want to know how well the good guys are doing against Darth Maul. Ergo, in the battle of Darth Maul vs random monster, it is important to arrive at the conclusion of the battle quickly so he might go on to face a “sell character”.
The “sell character”... this guy should be drinking in the spotlight. I’m on everyone’s back about bringing out the sell character(s), so don’t feel sad. Whenever your sell character is not on the page, you risk your reader escaping. The danger of reader-leak increases the longer your sell characters are gone.
A digression: The easiest way to bring out your sell character is to remove unnecessary frill characters around him. You see this in A Beautiful Mind which has 13 names for the entire story. This is really low, and an exercise in cast control. I’ve seen stories hit this number by chapter 1. It’s an unrealistic goal for your story which is bigger and affects more lives and more planets, but I just wanted to point out one of the techniques it uses to focus the spotlight.
[End-digression] The final battle is missing its sell character. Permit me to reach into your structure and suggest it shouldn’t be Caligula vs Realm. It should be Apollo vs Caligula or Apollo vs Realm. I think a perfect use case is that you have Apollo in the flag ship with Caligula in the other half of the Imperial fleet. Caligula defects mid-battle and it turns into a 3-way fight. Apollo loses his ship and you can do the space thing.
Again, why am I suggesting Apollo needs to figure larger in the main battle? You don’t want your story to climax on two non-sell characters (Caligula vs Realm). Someone needed to tell Lucas this too. One of his staffers should have been brave enough to ask the hard question: Does anyone care about a Yoda-vs-Palpatine fight?
I would recommend you don’t shelf Apollo and allow him to consume any bit of page Joseph isn’t using. I would suggest you don’t lose the tension of Apollo’s fear of discovery. That’s an excellent trick you don’t see often enough in fiction. Ride that horse until the final page like it’s a young colt that needs breaking in.
*Or... if you want this structure... sell Caligula from the start. Make him conflicted with his need for power vs his need for sobriety and inability to stick to one plan. Have him clash with Apollo on must more than the wrestling mat. Personally, I don’t recommend a trinary focus in any story, but I’ve seen it sort of work.
So, overall, I’m calling for more cohesion, a stronger central theme, an ending that services that theme, and more Apollo / Joseph