We came from SmoothMoves too. Never looked back. Spine is way better on many fronts.
And yeah, adding stuff like bones or new images or anything after you're done animating is not a problem at all. We do it all the time and it hasn't caused problems.
The runtimes are open source so if ever you do find bugs, or have some specific needs or ideas to extend it, you can read and modify the code.
But out of the box, unless you're doing some crazy things, chances are it already does all the things you need. And if it doesn't, these forums are always here too.
Just a note though, if you were animating flipping via scaling with SmoothMoves, you may have a bit of trouble doing the same in Spine. Animating flipping (horizontally or vertically) is also currently not possible except with a certain setup (via scaling where all bones have rotation = 0) because of the way Spine does scaling.
Other than that, Spine (especially Spine-Unity) is worlds ahead already.
Just to reiterate what Mitch said too, if you have some problems related to TK2D or Unity itself with shaders, materials and textures, it's mostly a separate issue. Spine is hooked up to use whatever material, texture and shader you give it.