I think it'd be fine to break backwards compatibility as long as you let us know what we need to do when we upgrade. :-)
As far as collision goes, I'm curious as to what you've done about it. I've just written my own collision detection engine since as you've pointed out, the Unity3D engine isn't so good for 2d collisions. I'm just about to see how my engine deals with sprite animations, but it's working great for static sprites.
Basically what it does is examine the mesh colliders created by 2DTK and eliminates the redundant triangles (since you had to make 2 sets along the z-axis to get Unity to detect collision) and creates a Vector2 array for the points and an int[] for the triangles. Then it uses some linear algebra to determine if any edge of one sprite intersects an edge of another sprite. There are some optimizations I need to put in, but it's working great for detection so far. I also have an alternate version that creates edges from the last frame position/current frame position so small fast moving objects like bullets can be detected without going through a sprite in 1 frame.
So... Since I've put in all that work I'm very interested in either having it continue to work or replacing it with your new detection system. Heck, I'd be happy to share it with you if it'll help at all.
And that leads me to a question I'll ask in another thread.