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It's unlikely that this cutscene will be of much help if that's what you want. It's probably easier to write your own cutscene from scratch - either way, it takes a lot of time, effort and programming skill to be able to create something like this. You need to be really familiar with ASM to have any hope of doing this. Knowledge of how to program in C would make this less painful.
Images one after the other would be close to impossible to fit in the ROM. I don't think that the GBA can even handle video codecs so compression would be difficult. All the animation in the Rayquaza cutscene is manually done in the code, with pieces being loaded and controlled by various bits of logic. I might do some research into this at some point though - it seems that even the special that plays it is undocumented :P