I just recently started playing this after a long while, and I had an issue in 2.4 where the cursor would randomly jump across the screen. Made it interesting when you were targeting an alien, hit fire, and suddenly you were taking out half of your team that was behind you!
I don't know if that was an issue that was fixed in 2.5 or not, but the reason that I am posting about it here is that I wanted to mention the variables that I exported from my shell.
I can't remember where I ran across this, I think it was a fix for a mouse issue in another game. Don't know what prompted me to go looking for it, but after uncommenting it, and logging out and back in, the jumping stopped, making the game much more fun.
# Fixes Savage mouse problems.
export SDL_VIDEO_X11_DGAMOUSE=0
Oh yeah, and my shell is zsh, and I run Gentoo, if that's relevant.