Before applying this solution make sure the "BigPicture Controller Configuration" for the game is set to the default layout (Zoë Mode Official Layout for MUA). To check follow these steps: 1: Right-click on the game from the games list of your library; 2: Click on "properties"; 3: Click on "controller" to see the controller settings for the game; 4: At the field "Override for Marvel: Ultimate Alliance" select the option "Use default settings"; 5: At the same screen, click on the link "Controller Configurator"; 6: Make sure you're using the button layout called "Zoë Mode Official Layout for Marvel: Ultimate Alliance"; 7: Apply the guide.

1. Download this file: CLICK[drive.google.com]

2. Extract with WINRAR (or other similar) to any place you want, and INSTALL the two Microsoft packages (This is a MUST-DO: The solution only works if Visual C++ Runtime 2022 is installed.)

3. Put the content of the folder "PUT THESE FILES IN THE ROOT FOLDER OF THE GAME" as it says (normally it is "C:\Program Files (x86)\Steam\steamapps\common\Marvel - Ultimate Alliance" - or ending with "...\common\Marvel - Ultimate Alliance 2"). Note: The files MUST BE in the same folder as the executable of the game.

4. Close everything, open the game, and finally have some fun!

***** This tutorial was tested in Windows10-64bit and with an XBOX-SERIES-X controller. If you are running other Operational System or trying to use this solution with other types of controllers, please, feel free to share in the comments your experience and let us know if it works in other scenarios.

***** If you are using a Playstation/DualSense controller, you might have to use this guide AND another additional solution, called DS4-WINDOWS (Thanks to Devaizter). More info here: https://ds4-windows.com/get-started/

What I did was just understanding the issue and searching for a software that would do the trick.
The problem is that Activision devs are lazy enough to announce and publish a "remastered" game without "remastering" its technology. The game, even its remastered version, is still based on DINPUT technology (and totally messed up with the mapping of the buttons, they never even tried to fix it), while modern controllers work with XINPUT technology.
The software was made by SAMUELGR and published by him on GITHUB as open source. Still, most of the credit go to him. I simply made the focused search for the solution and the final mapping of the buttons, as one of the infinite efforts of this community to keep this great game alive. The software is named XIDI, and it is awesome to make games with dinput technology to work with xinput controllers. You can find more about it here: https://github.com/samuelgr/Xidi