My $.02
Minnkota is the way to go in my opinion. After having owned both brands over the years i wont ever own another Motorguide again. My observations, a Minnkota is quieter, better in weeds, tougher, more reliable, better on batteries, steer smoother..... The only con with the Minnkota that i see is they are heavy. I have the Max pro 80 currently and i really like it alot. The lift assist is sweet.
My last motorguide i actually ran was on my old Champion(the one that came on my Nitro never hit the water). That thing was broken constantly. Busted cables, shreded pinion gears, bad aramatures, fried switches etc. That Motorguide only made it a year on that boat before i replaced it and in that time i was in the repair shop a half a dozen times. The Minnkota that replaced it still works to this day as my backup, it survived 8 years of abuse without any problems. I dont think Motorguide has gotten any better either, i still see guys in my club that have new ones having the same problems i had.
Overall i think i am very hard on the trolling motor, I use it alot and i use it hard. Motorguide has not fared well for me, Minnkota has taken every bit of punnishment i can throw at it.