Hello and welcome,
this issue keeps coming up, everywhere, we all understand what is happening and we agree. There are several approaches are doing this.
1. The legal approach, since at is core we want this project to be X-COM, the team uses the original art from a "legal" copy the user has.
2. The better approach, which we are trying, ask Take2, firaxis, or whomever is the copyright holder to allow us to use the names, text, etc... in order to create and 'improved' visually aesthetic game, while maintaining X-COM at is core.
3. The side step approach, modify all artwork, names text, etc.. as you pointed, however this won't feel like X-COM we know it plays like X-COM but it is not the same.
4. The f$$% approach, do whatever the team wants and forget who is the copyright holder and brace for impact. (not the preferred approach)
6. The mod approach, continue improving the game engine at its core and let user create their own mod, if that includes better graphics, music, text or whatever that is not out problem, we only distribute what is legal.
7. there maybe other paths that i have not thought of, but the programmers want to stay in the clear.
I am not a lawyer either, i and I also work in IP, we have attempted to contact the copyright holders as per trademark acquisition listing in the US. We are waiting for a reply, the project coordinator, has also attempted to contact them.
Disclaimer: although i am familiar with IP i am not very familiar copyright on the international level.