Hiya.

You might be looking at the Pro version...

Bones Animation is 'kinda' implimented...I think. I actually haven't really tried to use them, but they are in there.

Physics objects: Limited to 1 for Commercial, Unlimited for Pro version

Beam Generator: Again, Pro only for some reason.

Shader: Yes, if you know what you are doing. The SphereEngine .dll's you can buy will give you a lot of ooomph for your money. But again, if you really know what you are doing you can write your own .dll's.

I/O Port Control: Not sure what you mean here. But, again, if you know what you are doing you can write your own .dll's for this.

What kind of application / game do you have in mind to make? That might be a better way of getting some answeres.