I rather thought the redesign of Scarecrow was definitive.
...Bane looked much better...
Catwoman is a tough character to get right and I didn't much like either costume, though the new brunette Selina looked much better.
I agree with all these statements. The new Scarecrow was genuinely scary, something the old one never was. And not just the redesign, but the new Jeffrey Combs voice as well. It's a shame we only got one Scarecrow episode in TNBA. (And no Riddler episode, although the new Riddler design was probably the worst of them all, so it's no great loss.)
The DC comics set in the animated continuity did a story explaining the change in Selina's look. Basically, she discovered that the cosmetics company that made her blonde hair dye engaged in cruel animal testing. I don't know if they did one explaining how Penguin changed. (I'm assuming he got radical cosmetic surgery and liposuction.)
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.
Harley was fine, but I didn't like the new Two-Face look much. As for Scarface, both he and the Ventriloquist were radically redesigned. But the TNBA Scarface/Wesker episode was really good.