TL;DR: It is more difficult in the time-consuming sense, and usually no effect on GPA and WAM (unless you are aiming for 90+ WAM).
Long answer:
That is a tough question to answer...just thinking off the top of my head, your grade for the 3990 unit will be dependent on:
-Department: The other supervisors marking your work (some subjectivity cannot be avoided...)
-Project requirements: 'Bad' results are alright, but, you have to understand 100% what you are doing/have done.
-Your commitment/effort: The required contact hours is 12/week, although I have heard of both people spending less and more (9-5 every day, with breaks for lectures and labs, during normal semester), this really depends on your project and supervisor. I am clocking in 30-40 hours/week, but this is the Summer semester.
Finally, grades. In my opinion, if you are capable to do a 3990 project, a D is guaranteed; but, usually with effort it is a HD (80s).
Anyway, although so far it has been a tough experience, I have been really enjoying my time with research, so don't disregard it yet!
P.S. I forgot to mention before that the unit has to be in a biomed related (e.g. physiology) department.