I liked both films but what I disliked about '...Down Under' was that it feels like several subplots that only come together at the end - I liked in the first the fact that the mice and the girl strike up a relationship whereas in the sequel Cody only seems to acknowledge them at the very end when they're flying on the eagle.
I can't believe that no-one has yet mentioned the opening to '...Down Under'. With the exception of perhaps 'The Lion King' I think it's one of the most striking openings to any Disney film.