"...I took the exact same shot with my 5D Mkii with my 50mm, 200th at f11, iso 200, mine came out 3 stops darker and contrasty. WTF?..."
honesty, you are cracking me off when you are saying 3 stops darker (that means whatever slightly brighter than mid gray will become close to black). imo, one of the following could be the cases:
1. you have bought a lemon used camera, or
2. you do not how to use it properly, or
3. you have a bad instructor (go look for another one, hopefully your instructor is not cliff mautner. as if he is, then he is trying to tell you to buy nikon. but i do not believe that he is going to do that... and keep in mind that jerry ghionis has used canon 5d classic for years.), or
4. when he took a picture, he turned light on. when you took picture, he turned light off

5. tbd by people in this forum
i am not a pro photographer, but a dslr learner. i love to learn and analyze images/style/technical relates (try not to spend lots of money since my wife already starts complain). however, you can post your and his out of camera JPEG here and i can probably tell you why... but darker than 3 stops, please give me a break. both canon and nikon outcome good images. in day light, i probably can use canon t3 (yes, t3 not t3i) to output almost identical images comparing to your 5d mark II with one exception (dof)
i have been learning how to use a dslr in the past six months starting off from a t3, move up to 7d and buy a used 30d to help me to learn light every day after work, and recently order a 5d mark III to support low light learning and shooting at this weekend. i shoot at everything that has color and start to learn from there. i learn by picking brain from online sites.
attached is the image that i have shot with 30d (out of camera jpeg) the other day to show my friend. it could be brighter and cooler, but:
1. i will violate shutter speed, and
2. 50mm is sharp at 2.8; therefore, i am not willing to use 1.4 unless i have to
3. no more room to set kelvin temperature (minimum is 2800)
4. lazy to adjust white balance shift (i could adjust it by go further to blue and magenta to low down red tone)
5. iso already hit max, etc
note: could be more cooler color temperature...
if i can shoot that low light situation (one tungsten light bulb in my room) with 30d, i believe you will have no problem with your 5d mark II