only problem with changing the ani format is that you also have to change the conversin tool. there is also the problem of animation size. using 24 bit animations would use up 3 times more memory (as well as hd space, meaning a longer download time for your mod).
when doing animations i use photoshop 7 and open all the frames. then i paste them into a single image. i then crop out any white space. after that i switch its mode over to index color. i then save the palette. photoshop will assign the limited colors more accurately across all frames than using just one frame to generate the palette. using only one frame's colors could be problematic. lets say you have

of the color red throughout your animation, but hardly any red on the first frame. using the first frame as your only pallette source would not give you as many shades of red as your animation requires. i also never use a generic palette because you may end up with several colors on the pallette that are never used, and with only 256 colors, you need all of them.
i always save my animation frames as 24 bit rgb, then when i convert the frames to index color i set palette to custom, then i load the palette i created using the mosaic of frames technique discribed above. photoshop will mach each pixel up to the closest match on the pallette.
now if the ani converter could be upgraded to take 24 bit images and then calculate the best pallette based on all the frames, that would be good. i dont know if the code for the ani converter came in the fs source though.