For all I know Neobeo may pop in to say that JCS+ can get around this, but I seem to recall that animated tiles are limited to 64 (or 63?) frames, and I think you can only have 256 animated tiles period, assuming the tileset is small enough to allow you that many. It is of course possible that a level consisting of nothing but cutscene would be simple enough that you could go over the 1023 tile limit without too much danger.
I think the best bet is not to pretend it isn't JJ2. Use multiple scenes, have parallax backgrounds, layers, etc. Each scene can involve trigger scenery so you don't have to worry about animations starting at the wrong times, just the fact that only one speed is available. Lots of animations can be used more than once to conserve space. A full-out entire-scene-changes-every-frame video makes no sense at all.