I really liked this one.
I do think there are some modifications that can be made to make it fit in more with the site. For instance, I think the article would be more effective if it wasn't explicitly stated that we are looking at an imperfect Shakespeare clone. Perhaps his name can be blotted out for that effect. Maybe there can even be some ambiguity as to whether or not this is an actual genetic clone of the playwright. After all, there are circles of scholarship that debate his identity and his existence to this very day: even attributing his plays to other figures. It makes me wonder how they were able to get his genetic material and how they knew if it was right.
Perhaps that would make SCP-3564's fate even more tragic: in that not only did they keep making degenerated clones of him, but even the words that he so desperately feels a connection with and wants to communicate but can't due to his developmental issues aren't even his words, but those that his creators and handlers attempted to engender within him.
This way, as well, there can be ambiguity as to whether or not the failed clones were of Shakespeare or other English playwrights, like Marlowe: whom you do mention as a protocol.
But I really like the idea and the sympathetic nature of this one. The line about the failed clone without skin was also quite creepy and masterfully done. And I do agree with Roget that I would love to see records of his creators attempting to use him in a recital. And I so expecting there to be a CALIBAN reference. Or even a "If these shadows have offended" adapted into something like a protocol, or procedure. But good work. I hope you will continue developing this one.