I have the current high-end rMBP, and a friend of mine has the Mac Pro. Given your budget and uses, I absolutely think that the next generation (Broadwell) rMBP is the choice for you. The Mac Pro offers many incredible features and greater reliability with things like ECC RAM, but unless your courses involve large amounts of video editing in Final Cut Pro X you won't even begin to utilize the dual GPUs in the Mac Pro. Photoshop on the current rMBP just flies, has a great screen, incredible battery life, and, most importantly, the high end is within your budget. If you're buying a Mac Pro that you want to last for a long time, you would't but an entry level machine. Without any accessories, the cheapest Mac Pro I would recommend to someone is almost $7,000. For the rMBP, buy it with the maximum amount of RAM and SSD space you can get, since you can't change that later. CPU speed isn't worth fussing over too much. One warning I give is about the discrete GPU: it's fast, and I love it when I'm doing video editing, but it gets activated by a lot of things, and it will kill your battery life. If you don't need the discrete GPU, you might be better without it. Also, next rMBP may have increased support for 4k monitors, so that's a draw. The Broadwell chips are fairly delayed, so you might be waiting until around February for you new machine, but it's worth it. Broadwell will be much more power efficient, and that will mean a good bump in battery life/power. If you have any specific questions, feel free to ask or shoot me a PM. Sorry for the disorganized nature of this post, hope it helps.
EDIT: read more of what others posted about iMacs. I lean heavily toward getting a laptop, as managing two computers is a total nightmare and you'll need your computer more out of your room than in it. Once I'm out of school, my ideal setup would be to have a Mac Pro and a MacBook Air to have the most powerful computer at my desk (I do work that can actually justify the Mac Pro) and the most portability on the go. But as a student, buy a laptop.
That's why I'm skeptical about the rMBP. I'd get the discrete GPU model and right now it would probably realistically get about 7 hours of battery life. I'm assuming Broadwell will improve that, but who knows. If a $229 Chromebook can get 10 hours of battery life and is more portable, it makes me second guess not doing two computers. I could easily sync word documents with the Chromebook with Google Docs and it has a great web browser.
But I'm a little concerned at how the base Mac Pro is apparently the same benchmark wise as the top of the line rMBP. Makes me think that I should stop caring about reliability and take the free battery and beautiful screen. But I'm definitely waiting for the refreshes. They might make the 512GB SSD standard on the Mac Pro, which would decrease it's cost to me, especially after my student discount. It also might have more (and DDR4) RAM standard. Then I might see some more differences compared to the rMBP.
I totally agree that I wouldn't begin to realize the hardware benefits of the dual GPUs, but that's one of the reasons it's an attractive option to me because it means I have plenty of years before it degrades to the point where it becomes slow.
My question to you would be this, that others might also be able to answer: On the current MBP I have, I have replaced the harddrive twice, once was an upgrade and the other time it broke. I also replaced the RAM twice (once was an upgrade and the most recent time there was a defective chip). Do you think there is enough of a reliability increase due to the SSD and integrated RAM that it's unlikely to break, even after 5 or so years? Either case worries me, as the RAM means a new logic board, which basically forces me to get a new computer, while the SSD means a new card which is $400 minimum. With a desktop the RAM chip itself is $200 for a 16GB upgrade, and the SSD can be replaced with an external until I can afford a bigger chip.
It's nice to hear so many people's opinions!