Something from the big two
I suggest a Nikon F or F-2, or a Canon F-1 (old) or FTb, and a 50mm f/1.4 brand-name lens. The same reason I suggest everyone learn to drive in a car with manual everything: to strip away the excess and be in constant physical and mental contact with the raw basics.
IMO, Canon has the far superior metering system (built into the body, 12% patch that takes 100% of reading, while Nikons were equipped with optional averaging or center-weighted averaging meters, which have to be properly coupled to your lenses and usually don't work these days anyhow), and Canons are more simple to control with very limited knowledge, and changing lenses is a breeze. All you have on the camera are a few basic controls. They also have what I believe to be a superior lens system, with certain fast lenses that Nikon never had. Of course, this is only a make or break issue for those doing low light stuff, where half a stop does matter. For your run of the mill student, the differences in the lens systems between the two brands is negligible.
I find AE-1s to be confusing, personally, and a poor choice for establishing a solid foundation. They are fine cameras, but require an intelligent and highly disciplined approach to really get the basics down, since they are so dumbed down compared to an F-1. In order to use an AE-1 intelligently, you really need to be coming from a manual camera anyhow.
They are fine cameras, and can get the exact same results as any pro model...but they do not support rigorous study of the technical basics. They were and always will be more of a convenience for the masses rather than a thinking person's camera. Please don't take this the wrong way. They can be masterfully controlled as well as a pro body by someone who ALREADY knows what they are doing, but are simply not the best learning tools, IMO.
The huge benefit of Nikons is their availability, and lens compatibility. Canon FD is an excellent but orphaned system.
I am a Canon FD guy at heart, but I absolutely love my Nikon F. I have a hard time recommending one over the other...but I love being able to adapt my lenses to a wide variety of other systems...which you CANNOT do with Canon FD. I also prefer the Nikon rotation of the focusing collar and aperture control ring vs. Canon/Leica/Minolta, etc. It is more intuitive for me going right for infinity and right to stop down.
In short, if the beginner will also be using digital some day, I would just suck up the lens speed disadvantages of the Nikon system and go for a pro-level Nikon (F or F2) with AI lenses.
If the beginner wants a heck of a deal, needs the fastest of the fast lenses, and doesn't mind an orphaned system, Canon FD can't be beat. Nor can Nikon Fs for bang for the buck on the used market...but their straight F lenses (AKA NAI or pre AI) are also an orphaned line, unless converted (or used on the D40 or D40x with manual aperture and no meter). Later lenses can be used on the F bodies, however.
Any other brand doesn't offer anything that Canon or Nikon don't, IMO. Great cameras from several other brands, but not much point unless one gets an EXTREMELY good deal. Having a total system counts for a lot, and only Nikon and Canon have extremely extensive ones.
I also highly suggest pro bodies. At this point, they are so similar in price to amateur bodies that the difference in price is worth paying in order to get the extra features/extended system compatibility.
Quite honestly, the basic differences amount to nothing. A smart person will get great pix with either, and vice versa. Just try to think of them as educational tools. You don't necessarily want the easiest-to-use camera or the camera that simply gives you acceptable pix most of the time via automation. You want the camera that teaches you the most. This is usually the camera that makes you work the most and think the most. It all boils down to time and effort devoted in the end, no matter what you use. No matter what you have, you have to work a lot, spend a lot, and study a lot...and be disappointed a lot, but be able to recover.
You can easily get an FTb and 1.4 lens for $100. Nikon F with a 1.4, probably $100 to $125. At that price for an F, no sense at all in getting a lower-end model. Canon F-1 or Nikon F-2...a bit more. Maybe $200 to $350 depending on condition. I got lucky and bought an F-1 with a Vivitar Series 1 28-90 f/2.8-3.5 macro for $99 in a pawn shop.
2F/2F