New feature upcoming in AeMe2... A 'transparency' setting for thumbnails. AeMe will automatically detect whether a picture is a transparent PNG, transparent PNG or alpha PNG, and if it isn't, it will apply a box shadow to the thumbnail. Believe me, it took me some time to figure out how to determine 100% whether a picture is transparent, ah ah.
Anyway!
I also fixed the upload of animated GIFs using ImageMagick. Yes, it was broken. I guess nobody uses ImageMagick. Which isn't surprising, as it's buried in the admin settings.