I rather thought the redesign of Scarecrow was definitive.
Freeze looked good (though he looked even better in Batman Beyond), the Joker, I honestly didn't like any less than the BTAS version, since I have issues with that version too (again, BB improved on both.) Penguin, as has already pointed out was much improved, Bane looked much better, as did croc, Nightwing and Robin were both a welcome change. Poisen Ivy is a tough one since I see the new version showing how she'd become less and less human, though oddly I wish they'd made her barefoot like in "Almost Got 'Im", she never looked better than she did in that episode. Catwoman is a tough character to get right and I didn't much like either costume, though the new brunette Selina looked much better. Most of the others (Harley, Twoface, Scarface) were for the most part unchanged, so I don't think the change was as bad as some seam to think.
Either way, by the time they got to JLU I think they had the "perfect" style for the subject matter, at least within the constraints of format, budget and time.