Looking for a more suitable animation tool

Question

I've been creating animations from sprites in After Effects, with mixed results.  The input is a number of pixel art sprites (exported from elsewhere), and the output is a video, characters running around and interacting.  I have AFX doing quite a lot, but it's very awkward and I'm pretty sure it's the wrong tool for the job.  Can anyone either suggest better approaches, or more suitable software?  I'll describe what I'm doing now:
- Many sprites are bodies or heads to combine, eg. a smiling or angry faces and walking or standing bodies.  I set the head position for each body sprite, so any head fits in the right place on any body (trivial rigging), then apply it with a script, so I can change the body and the head moves to the right place automatically.
- Some sprites have multiple layers.  For example, while heads are normally on top of bodies, a body may have an arm raised, which needs to be above the head instead of below it.  I can create the extra layer for the body separately, and it works for any head.
- I can set the draw order per-layer.  Usually, one character and all of its parts is drawn on top of another--body1, head1, body2, head2.  But, if two characters collide, handshake, or interact in other complex ways, I may want to draw both bodies, and then both heads, even though the heads and bodies are still anchored normally.  Some sprites may have multiple layers, eg. body, head, hands, legs.  (Z position hack...)
- Individual layers can be adjusted separately, eg. to adjust the default head position downwards to give a nod.
- Some sprites are hue shifted (hair color, clothing color) or have more complex adjustments applied, so I can reuse more sprites.
(I'm only describing what I'm doing and not how.  I wrote more detail about what I'm actually doing in AFX and the specific issues I'm having, but it was too long and people can probably already guess the practical issues of using AFX like this.  I'll post more info if anybody asks.)
The result is functional, but a real hassle to actually work with.  AFX is a compositing and effects tool and it's not really designed for animations, and only its scripting support has let me abuse it this much.  I don't know of a better tool, though--searches for animation tools mostly come up with things like Spine (authoring individual models for importing into games), and nothing suitable for creating complex video animations from sprite sets.
There are probably many tools to do small pieces of this (sprite animation sequences, effects, scene animation, camera), but I'd really like to not split into a multi-tool workflow, since I want to experiment freely with a scene, not lay out an entire scene and then create it start to finish.  Does anyone have any suggestions (or better places to ask)?

Answer 1

There are many other DTP applications:
http://www.freeforum101.com/iworktipsntrick/viewtopic.php?t=137&mforum=iworktips ntrick
You have to be more specific about what you are looking for.
Peter