On the smaller transom mount motors, you will probably be alright with either one, due to the simplicity of both. The larger ones are a different story. But, here are a few things to chew on.
Minn Kota has Maximizer as an option. I am not sure about the Varimax, but I know on many of Motorguide's motors, they don't have that available.
Minn Kota will very likely make it through the recession we are facing now. There has been much talk of Brunswick (owns Motorguide, among about 30 or so other boat manufactures) going under. I personally see it happening, as Brunswick in the past 5 years has employed many of the same management methods OMC did in its last 5 years. Then, when they accidentally introduced a bad motor, they couldn't make it through. In this case, it isn't so much of the bad product that will kill them, but the economic state. It took the financial loss of the Ficht motors to kill OMC, and this economy is showing the same loss on Brunswick right now.
If Brunswick goes under, who will support warranties?
I am not going to bore y'all with it, but if wanted, I could present quite a bit of statistical info that (I hate to say proves, as it pertains to my opinion - I guess we could say support) my opinion on the MK motors being an all around better motor, on many fronts.