Modding XML2 actually began sometime in late 2005 (well before Activision announced Marvel Ultimate Alliance).
The first marvel mods were new skins and modifying game-save files to play as NPCs (ie. Archangel).
If I remember correctly, idrinkdrpepper, darkmythology, Tetragene (the Dazzler fanatic) were some of the earliest modders on GameFAQs. There were no XMLBCUI or SKINNERUI to (de)compile your stuff. The only mod tools were TextureFinder and your favorite hex-editor. That's why I call those modders "stone-age" modders. 
Yes. I remember these times. I was a member of a forum called "Haven of Apocalypse" (along with Tetragene) that was following the X-men Legends series, and I was told about someone on GameFAQ that had hex-edited the save file so that they could play as Archangel. So, I went to the GameFAQ board to see how to do that (my GameFAQ screenname was nightcrawler329). I think this was late October 2005. Once I learned how to hex-edit the save file (very easy), I uploaded a video of it to youtube. Actually, I created my youtube account specifically for that purpose.
The community of modders at GameFAQ was small at that point. We were pretty much just poking around the various files using a hex editor and seeing which ones could be swapped and edited. I remember Tetragene (who was also a member of the Haven of Apocalypse Forum) and I were editing the Effects files and trying to change the names of the characters.
I think a few months later, I had figured out how to edit the skin files using Texture Finder. Since I am not a programmer, the process of editing a single skin file was a painstaking process. I remember Tetragene, Kinstryfe, Youngblood0000, and Darkmythology had sent me some edited texture bitmaps that they wanted me to insert into the skin file for them. I think I did a few of those, but then I wrote up detailed instructions on how to use Texture Finder + Hex Editor to make custom skins. I also compiled a short instructional document about how to hex edit your X-men Legends II game. Youngblood000, helped with that. He also created a download directory of all of the customized skins that people created. As a matter of fact, Youndblood0000's web site is still up
http://thegamersjournal.com/rpg/pc/xmenlegends2/At this point, I think the modding community was still active in making more and more customized skins, but I took a break from it in anticipation of the upcoming Marvel Ultimate Alliance game. When MUA came out, I went back to the GameFAQ boards to see if people were modding MUA. I remember Noelemahc was kind of the person running things, along with thetommyboy2002, blizz, and darkmythology. I think they had identified that the herostat file as the one which governed the playable character roster. They were also able to unlock Colossus and Moonknight by transferring some files from the console version (I believe?).
I started getting back into modding by trying to decode the herostat file. The issue was that the only tool I had was the hex editor, and when you open a .engb file in hex editor, you see a bunch of unintelligible hex strings along with some words and numbers. Eventually, I figured out how to parse these files. But, since I am not a programmer, I did it all by hand (translating one hex string at a time). Thankfully, a user named
nba2kstuff came along. I described to him the method of how to parse .engb files and he created an awesome program that could edit them. I think it was around this time that THX started marvelmods.com.
nba2kstuff also created a program that automated the skin-editing method, so that it no longer had to be done via hex editor. So, I do think nba2kstuff deserves credit for getting the ball rolling, because his editing software really opened up a world of modding possibilities.
