I too have experience with both brands. Hands down the MinnKota is a better trolling motor, period! They have the smoothest foot controls that I've ever used.
I have owned 2 Motorguide's and had problems with both ranging from fried wires which happened because they didn't use tie wraps and the wires eventually started to rub metal. NOT GOOD!
Another problem that I had was with the steering cables. My leg would hurt me for hours after a day of fishing because the cables were binding up.
Go with MinnKota!