They definitely both have their good and bad points.
I prefer the cardio stuff on My Fitness Coach - proper aerobics class which is pretty good fun and I'm loving that it can incorporate your equipment such as step, weights, HRM. I just did a 30 mins step aerobics class and it was bloody hard work! I then thought I'd try the Wii Fit Step Plus using my step as the Wii Fit board you'd barely notice. Was ok, but My Fitness Coach was definitely a better and more interesting workout. With better music!
However the yoga is miles better on Wii Fit imo. I like how they talk you through the timing of the moves, as in a lot of cases you are in such an angle, you can't follow it on the telly screen. My Fitness Coach talks you through once only, so for the rest of the moves you have to do it from memory, or contort yourself to try to see the screen. Not good.
You also cannot pick and choose your moves within your workout on MFC. You select for example 'upper body' and then follow the workout for 15/30/45/6o mins. Ok for aerobics but for me with my bad neck, there are some yoga/muscle workouts I just can't do, but if they come up in the middle of MFC workout you don't have an option to avoid them and have to just sit it out. Wii Fit lets you choose the moves you want to do - albeit one of my complaints about Wii Fit is the stopping and starting due to going in and out of exercises!
It would be perfect if you could choose the moves you want in either programme and then they are put together in a custom programme for you so you don't have to chop and change.
Maybe someone will think of that some day :D