Welcome to the forum, spidermatt.
You're asking for quite a lot there, aren't you? Judging by what you've asked for, I have to assume that you're the same person as "MarvelousMatt" over at YouTube who has made videos asking for the exact same things. I'll address each of them.
If
Electro was a boss character in your EXG Mod, what level would he be in?
This being a hypothetical question, I would place

Electro somewhere in the New York City mission, because he's a Spider-Man villain. However, there's already two bosses there who's connected to the story.
And for
Wolverine in Iron Man Lab and Warriors' Hall, can you replace 0301 with 0305 in the npcstat, just like you replaced
Iceman's 0801 with 0810. And can you replace the Doombots (13501) in Murderworld with the actual Doom Sentries (7001, 7002, 7003, 7004)?
Changing Iceman's skin made sense because he's laying on a couch at the Sanctum Santorum, so he wouldn't be in ice form there. Changing Wolverine's skin, however, wouldn't make sense because his T-shirt & jeans is what he wears in every cutscene and every briefing of the game. As for the Doombots into Doom Sentries, I'm afraid I cannot because Murderworld is VERY sensitive. Adding or changing things in that mission can break the game. It was very difficult for me just to add that extra stage to it, which is why I added nothing else to that mission.
And for music, can you change these for me please?:
New York levels (ambience and action) - https://www.youtube.com/playlist?list=PLO4jlmGoc6uBD5b3YDG-EalAmP6MquxWW
Astral Plane levels (combat) - https://www.youtube.com/watch?v=W3jrnnl2dys&pp=ygUaeC1tZW4gbGVnZW5kcyBhc3RyYWwgcGxhbmU%3D
Latveria level 2 (combat) - https://www.youtube.com/watch?v=RDHJ5Jr0klQ&pp=ygUeeC1tZW4gbGVnZW5kcyBzZW50aW5lbCBmYWN0b3J5
OK, with those requests, you're likely wondering why I didn't pick each and every music track from X-Men Legends 1 and 2 to match those stages when I created the EXG. The reason is because...
This isn't X-Men Legends. This is Marvel Ultimate Alliance. I didn't want to add ALL of the XML1 tracks because then it would feel like you're playing XML1 and not MUA. That wasn't the goal. The music of the stage changes the feel of the stage, so while I did choose some XML tracks for nostalgia, I didn't want to choose all of them. Plus, some music I chose such as the combat stage for the Astral Plane better matched the darker, horrific environment. Latveria? Keep in mind that you're in Latveria, not the Sentinel Factory, so different music, different feel. You see what I'm saying? In short, it was an artistic choice.
Also for Loading Screens:
Stark Tower - Unused Stark Tower Artwork from Enigma's MUA1 Bonus Official Loading Screens
Level 3 (Omega Base) -
MUA Hulk Loading Screen
SHIELD Outpost - Atlantis art from Blizz's
Namor Mod (found in textures and loading)
Castle Doom or Big Top (Murderworld) -
XML2 Dark Phoenix Loading Screen
Egypt (Time Warp) -
XML2 Apocalypse Loading Screen from Emigma's Bonus Official Loading Screens
Asteroid M (Time Warp) -
XML2 Magneto Loading Screen from Enigma's Bonus Official Loading Screens
OK, my reason for loading screens is also an artistic choice. In the Omega Base, you're fighting Hulk, but he's not really an enemy, you know? (Plus, they don't know that Banner's turned into the Hulk yet, so adding that loading screen ruins the need to talk to Reed Richards.
I'm not going to add that Dark Phoenix loading screen because you're not fighting the Dark Phoenix, you're fighting a mind-controlled Jean Grey -- big difference. Arcade wouldn't be able to control the Dark Phoenix... no one can. Dark Phoenix is powerful enough to be the final boss! Thankfully, that's not who you're facing in Murderworld.
And just so you're aware, if you add too many loading screens for bosses, you know what happens? You won't see the loading screens for your playable roster because they're being blocked.
As for not adding Apocalypse and Magneto loading screens, again, this is not XML1 or XML2. I chose that portal loading screen I made because I'm telling a story that you're trapped in a time warp. Have you noticed that the portal loading screen are the exact same colors as the portal found in Doomstark Tower? It's the same portal. That loading screen shows the player going inside and traveling through that portal back in time. So, to change that to Apocalypse & Magneto loading screens takes away from the story I'm telling.
Whew! Alright, I think I covered everything. The
Expanded Game (EXG) mod I made is further telling and expanding the story for Marvel Ultimate Alliance, and not just adding stuff for gameplay. I wanted to expand MUA, not merge it with XML1 or XML2. I hope you understand the artistic expression I created with this EXG, are enjoying it, and are not too disappointed that I can't fulfill your
many requests. Storytelling is very important to me, and I can't sacrifice my vision.