As I said, it's still starting and needs some tweaks...
The developer is resolving the 2H vs 1H + OH issue as far as I know and some other things. Spirit to hit conversion sounds easy to correct.

About enchanting, also as far as I know, the only issue is hit enchants. You can try subtracting the amount of the ones you might use from the cap to get your results. I agree this is not a nice solution, but it does the job although you might have to run the optimizer more than once... As of the last I read, the dev is not planning on adding enchant support for now (except the OH one), but I do believe he will end up changing his mind at least for the hit enchants although I can't vouch for him...

About soft caps I really can't say... I'm not sure how Mr Robot deals with them either... This surely is unsolvable with only stat weights. If you wanted to deal with this perfectly, you would have to give the program the exact scaling function of said stat and not just a single number. I doubt Mr Robot handles this well but please correct me if I'm wrong.

Most of what you mentioned are either bugs or features that are easily solved/added to make the tool better I think. And if they are, it will probably make it better than Mr Robot for finding the best solution and not just a very good one.