Stage3D is an API not a frame
Stage3D is very low-level and other 3D engines build on this to create an easier to use framework. This includes making it easier to do reasonably complicated features, including lighting, shadows, importing models etc etc
Strictly speaking you can use just Stage3D without any framework at all, however if you are doing anything slightly complicated you will end up writing your own framework.
I would recommend using a framework.
there are loads of frameworks out there you can take a look at. some are free other aren't, some have license agreements requiring you to include framework logos etc.
yes you can make and animate 3d content with stage3d although if you are going use stage3d without a framework it's going to be very hard and complicated.
tbh i have only ever used papervison3d (before stage3d came out) and i would not recommend it now.
recently I have been playing around with pure stage3d so i can understand what's happening low-level under the bonnet of these frameworks and believe me it's been fairly complicated getting even the basics working. in doing my research flare3d and alternativa have been the engines of choice by those that have been working with the frameworks.
perhaps you could read this which is probably better than anything i could give you