Personal opinion - note that my experience w/Milkshape is a year old:
From my own experience using both AC3D and Milkshape, AC3D is a much more robust and capable 3D modeling package.
If you're developing for games, the ability to add object "properties" in a text field is invaluable (each object can have an associated text field, accessible via F9 in Object mode). With the registered version, you get a wider range of export/import filetypes, plus you can use the SDK to write your own. I haven't used Milkshape's SDK, but AC3D's is very easy to learn.
AC3D also allows you to create _much_ larger scenes than Milkshape (I believe you're only limited by available memory). Also, I believe AC3D has a better set of editing tools than Milkshape.
Another advantage from a gaming perspective is that AC3D can be used as a level editor. With the SDK, it's *very* easy to get level data into your own custom formats, or you can export using an existing common format (although most generic formats won't take advantage of the "data" fields for adding flags/etc to your level data). You can also create highly-detailed models and use AC3D to create cut-scene data for your games (although you'll still need to export to another format for animation/rendering).
The one thing Milkshape has over AC3D is animation support. However, if you're using CharacterFX to animate, you may not care so much about this. I use a different animation package, but I believe AC3D exports to all file formats importable by CharacterFX, so getting your data there should be easy enough (plus AC3D and CharacterFX each have an SDK if you want to export + import your own file formats).
I've evaluated quite a few 3D packages, and I've settled on a combination of AC3D and Blender for all of my 3D needs. While Blender is technically robust enough to meet all of my needs, I've found AC3D MUCH better for creating and editing my base models, and I use Blender for animation + rendering. I find that AC3D has struck a good balance between easy of use and powerful features.
Support for AC3D is very decent - The lead developer (Andy Colebourne) seems to be on the boards nearly every day, and someone usually answers questions within 24 hours or so.
Good luck - hope this helps,
Dennis
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