1. Cutscenes are not anis. In the original exes they are mve files that we can't make. The fs2_open exes intend to have support for DIVX avi files. (I'm not sure how complete that support is right now, but I've heard mention of Windows versions using DirectShow to play avi files.)
2. Pre-mission briefing cutscenes are set in the campaign editor. I'm not entirely sure if it will work because I've never tried it. If it doesn't, it can be fixed.
3. Currently, FS2 doesn't support post-mission cutscenes except for special case situations. (The end of the main FS2 campaign.) That could probably be changed if/when cutscene support is finished. (Or at least when the interface to the cutscene system is finished.) Again, I don't know how things stand on the avi support.
4. Changing the cutscene played at startup is simply a matter of making an overriding intro.mve (or maybe intro.avi) movie and putting it in the right spot. I'm not entirely sure where it would go, but I'm sure someone else knows. (It might just go in the regular game folder with the exe's and VPs.)