Sounds like you two should stop wasting time with easy courses. If you are as brilliant as you say, there is no way you can't get permission to skip prerequisites or transfer out.
> The best courses are the ones that allow you to swap a midterm grade for any missed homework
My recommendation: do the homework - you'll presumably breeze through it if you have mastered the material. If not, it will be a good refresher.
At many universities, students can also customize their course plan with department approval.
Usually you can take graduate courses without having completed the undergraduate prerequisites if you talk to the instructor. Perhaps you might find that more your speed.
If graduate courses are trivially easy for you and you've exhausted them all, you might consider taking the Ph.D. qualifying exams and moving directly into research.