Fellow first year engineering student here,
I previously owned a Surface Pro 3. I decided that I did not enjoy the flimsy, "clackity" keyboard was not worth the amount of money I paid. In general, the form factor of the surface did not suit my daily productivity needs as a college student. The keyboard of the Yoga is very solid and professional feeling. The trackpad on the Yoga is far superior as well, offering a larger touch area, more touch accuracy, and more customize-ability. What do you expect? Lenovo has been perfecting the form factor of their keyboards and track pads on the Thinkpad line for decades.
As far as a pen goes, I did not buy my Thinkpad with the pen feature, as it was not required for my schooling, and I hardly used it on my Surface. HOWEVER, the functionality of the pen on either device should not be a problem. Both pen interfaces are made by the same company, so if you buy the Thinkpad with the pen feature, it should work just as well as the Surface.
I found I much preferred the feel of a solid laptop in my hands and on my lap. The fact that the Yoga can bend back into the form of a tablet is a great bonus. It may not be as practical as a normal tablet, considering that in this form it is thicker and heavier than your average tablet, but it certainly does the job.
I use the "laptop" mode much more often than the "tablet" mode, so it seemed having a device with an excellent laptop feel and a manageable tablet mode (the Yoga) suited me better than a device with a flimsy feeling laptop mode and a definite focus on feeling like a tablet (the Surface).
The hardware performance on both devices is excellent, I have had no qualms with either one. So the main thing to focus on here is the form factor of the devices, as I have commented on earlier.
I ended up selling the Surface and bought a Thinkpad Yoga 12" instead, in a similar configuration (i5 4200 instead of 4300, negligible difference in processing power in my opinion, with a cheaper price tag).
If you want a tablet that can be a decent-ish laptop, buy a Surface. If you want a laptop that can be a fine tablet, buy a Yoga.