I haven't used format factory much, I've always used 'Jasc Animation Shop'
To change resolution in FF thou, once you click 'All To Gif' Click 'Output Setting' under video stream tree, Click Video Size and manually type in 960x540
It's hard not to get color loss with an animation like this, with all the pictures it cycles through, a 256 color palette isn't going to work too well. I didn't like the results in format factory just converting the whole video, when I tried with Animation Shop converting the whole video I had much nicer results, thou still some color loss.
There's around 300 frames, you could split it up into smaller parts, say 20 frames each segment, or possibly less, add frames until you start getting color loss. (I just tried this, probably going to be even less than 10 frames per segment to keep all colors)
I had a go of the marvel intro using 'Jasc Animation Shop', here's the file I made, 13mb filesize, some colour loss but still looks pretty good. This is converting the whole video without splitting it up. If it was split up into segments in full colour, OTOH you would probably end up with 30mb of .gif files or more.
FILE -
marvel_intro_gif.rar
If you're not happy with this result I can try split it into segments for you, this will take some time thou.
.GIF for cutscenes is a real problem for high-res mods, at 960x540 cutscenes become huge in filesize. I have 200mb of scenes in my mod atm, just for an intro segment.
untunnels suggested a while back it might be possible to add .OGG video support to openbor. hopefully something like this is added one day.