I gotta give you credit....
I was skeptical during the opening, but the movie ending up being a pretty sweet watch. You recreated all the attacks nicely, and blended your animation shortcuts(as many as there might have been) considerably smoothly amidst all the action. Although, I must agree that you did put a lot of focus on visuals/effects....(i.e, flawed storyline, captions,many overdone explosions).
On a second note (maybe its just the way that style is, or maybe its just me) but if I had never familiarized myself with Chrono Trigger, and watched this movie...I'd think that Lucca, and even Flea(like she/he really is supposed to be, but that you did not mention in this movie) were simply male. Don't want to nitpick, just thought I'd mention it....
P.S. Why would you not reference DBZ? They both have the same art director.(Akira Toriyama, was it?) Anybody who complains about that should have the Delta Attack performed on them. :)