Mr Clever would certainly be an exclusion - he is the Doctor. The Ganger is a grey area, as a separate entity, but I think, yeah, as a direct copy probably not really eligible - not really within the spirit of the thing, even if technically in the letter. But there are literally 100s of minor characters just waiting for their chance in the spotlight, so I'm sure you'll be able to think of something else - or find a prompt to inspire you!

And, of course, any characters are welcome in the fic, it's just that the focus (or equal focus) needs to be on a minor character, so you can write still write about any Doctor, Master - or one of the other characters from that ep with the Ganger Doctor. :-)