For a 3d collision detection , Bounding Volume hierachies (BVH) would be a good approach to narrow down on specific potential geometry to test against instead of testing against the entire 3d model (ie. narrow down to specific bounding box leaf which a conservative coarse sweep velocity volume intersects with..).
But of course, the scene graph woud still be generally 1 combined single model... (seperating it out to seperate meshes will add to draw calls which isn't good for performance.)
I have a 2D version of BVH ported over from original wonderfl source http://fl.corge.net/c/jA37
https://github.com/Glidias/Asharena/blob/master/src/alternativa/a3d/cullers/BVHC... (scroll down to BVHCulling
I didn't convert it to a HAxe generic yet though. Woudl likely need to replace the proxy:T to a generic data type, and converting it to haxe should be pretty trivial.