if you need full layered animation that's beyond a simple animation program. Try tvPaint, or ToonBoom or Pencil... there's a bunch more, some more raster oriented, some more vector, like AnimeStudio, some are a mix of both.

http://www.thebest3d.com/animationsoftware/

Dogwaffle can do animations but you're right, not animated layers (and neither opaque layers). It's a paint program first. But you can also achive lots through the custom brush, including to keyframe a path and transform of a brush to be rendered across an animation. The brush can itself be a animbrush, i.e. carry a image sequence or something coming from a video. You can paint with video on video.

Many tutorials will show examples at www.thebest3d.com/pdpro - lots of postwork examples. keying (blue screen/green screen) of poser walk sequences, etc.

But granted, it's not a replacement for After Effects ;-)   at least not for a bunch of things.

Back in the days of Amiga, D-paint (DeluxePaint) was a great little proggy, which inspired Dogwaffle. Another program, more for video and animation, has probably inspired tvpaint. Or perhaps that one started there as such, I don't remember, mix them all up in this old brain (no wonder they call it grey matter,... not much left there in distinct shapes and colors LOL... I now call it the cyborg's alternative to RAM (Rand Access memory) and ROM (Read-Only memory), it is FOM: Forget-Only Memory

oh, and there's one more which may just be what you're looking for, and we actually like it and use it in making icons for Dogwaffle. It is called Cosmigo Pro
Look for it at http://www.cosmigo.com/promotion/index.php

Pro Motion by Cosmigo also has a number of features found in Dogwaffle such as Swap buffer. Similar shortcuts for accessing some of these features that were seen 25 years ago in Dpaint and I think you'll like it.