Massively comes down to personal preference because once you've made your decision, you're pretty much stuck with it as changing body and the lenses for another make gets silly expensive.
You say that but I am in the middle of selling all my kit. I have only lost £20 on two lenses (Canon 70-200 f4L & Sigma 30mm f1.4) with three years use out of one and nearly 2 out of the other. The only loss I am really going to take out of the whole thing is the camera body, but they depreciate regardless of which system you use.
As I am selling out, I was tempted to jump over to Nikon as a mate of mine uses a D700 and has some outstanding glass that I would love to get my hands on (NOCT 58mm f/1.2 anyone?). Its only because I am getting a bargain that I am staying with Canon, and with only two lenses left, it will always be easy to sell off and move over at some other time.
For a beginner, you just have to know whether you are going to be happy "just" taking snaps or whether you are going to get bitten by the bug and end up spending ££££'s on glass etc.
A guy at work just bought a new 500D, he wants a new lens for it and was talking to me about them and what I am selling. He does not care about
L this or f1.4 that. He liked the look of my 24-105 but was shocked at how much it cost and laughed at the thought of spending that much money on some glass.
He is buying himself a 18-200 cheapo Tamron/ Tokina lens, is not fussed about having the sharpest shots in the world and just wants to be able to snap away whenever, without any hassle.
If you fit in to the "happy snapper" camp, then buy a camera/ lens package that offers the most bang for buck. If you think that you will want to progress through glass and bodies, then you are better off buying into Canon or Nikon.
It is also worth looking at the second hand glass/ bodies. There are some bargains to be had, and second hand glass hardly ever looses value if bought wisely.