Better? I love them both! Fantasia 2000, IM{ns}HO, was a return to the best of Disney anamation. And it may be the last time, in a long while to see the wonderful work of Eric and Susan Goldberg (sp?) (Flamingo and Rhapsady in Blue segments), since they have both left the company. OTOH, Fantasia was conceived and produced by Walt Disney himself, with the Philadelphia Orchestra c under the direction of Leopold Stowkowski. This is not to say the James Levine and the Chicago Symphony isn't also wonderful.
That said - your question seems to be "which one would a 5 year old prefer"? I would go with Fantasia 2000 for the folowing reasons. The seqments are shorter, and more contemporary, more likely to hold a 5 year olds interest. There are also appreances by "guests" ie: Steve Martin, Teller & Pen etc. likely to amuse (I found most of them a distraction - but then, it's been a while since I was 5). Also, since Fantasia 2000 doesn't have the "Nitght On Bald Mountain/Ava Maria" segment, there isn't a real villian - the Jack in the Box can be a bit scary, but not as much as Chernabog.