Research paper was terrible even with high skills

AFAIK the first draft will always be set as Poor. If you edit it, it should jump up to Excellent. Similar deal with the presentations, they'll always start as Poor and can be refined twice. When you get a message saying something like '(Sim) can't improve this project any more, but continuing to work on it will help boost their grade', you can submit it (or keep working on it for extra performance in the class, if you're doing badly).