I would get the 15"...just because I have one, so I am a bit biased.
The whole nVidia issues is big, but it isn't that bad. Don't listen to the people that say that your card will fail, because that isn't true. A lot of people here have yet to have any problems with their 8600 (including me). I am not worried about it at all because I have AppleCare and Apple is standing behind this for 3 years or more. I don't have a problem with knowing that my video card *might* fail. When it does, I am fine with that. Cards will fail, chips will fail, hard drives will fail, logic boards will fail, it's a computer!
On a tech stand point, the 13" MBP out performs the 15" MBP, CPU wise. But, video wise, I would much rather have a discrete video card. On top of that, the 8600GT outperforms the 9400. The 9400 also shares memory with the main memory, which to me is a disadvantage. The 15" can support 6GB, while the 13" can support 8GB of RAM. Hard drive isnt that big of a deal, you can change it on the 15", just dont break anything.
Screen wise, the 15" is larger and has a better resolution. They are both LED. You also get an express card slot as well as firewire 400/800. The unibody has SD card and firewire 800.
Next, battery and design. The 15" has a removable battery while the 13" has a 7 hour integrated non removal battery. The 15" is the classic PowerBook/MacBook Pro design while the 13" is the unibody style.
What is all boils down to is the price, and what you are using it for. Depending on the price, you might be able to get a refurb 15" unibody for the same price.