In such a competitive industry. It is no longer which camera is better or lousier. You have to look at it in terms of Budget and Needs of yourself. Companies nowadays input features based on market research that they think would appeal to a certain customer segment.
Lets say you have a budget of 1.5K ;then source out cameras that are +- $100 along that price. Similarly, are you going to be printing large pictures? (this would ans the megapixel qns). Perhaps you should think about what you want and need first.
The 50D is not compared to the D90. In fact if you go to dpreview.com (a very popular review site) and read its review of the D90, its compared to the 450D.
I think in this day and age, it's not so much what is better or worse but what suits you. This is because there are almost no rival cameras that are better or worse. Majority of them have good and bad points that cancel each other out. Of course the comparison of cameras has to be in the appropriate segment. No point comparing a EOS 1D with a Nikon D60. (I hope you get my point here)
You should also think long-term. If photography is going to be a long-term hobby then you should consider getting a higher-end body(whatever brand tt it is).
No point getting an entry level SLR then end up regretting because you are craving for a better machine.
To be fair you shd read as much as possible about both cameras and make a decision. In the end it might be something really minor that might let you choose one over the other.
Asking which is better is like asking to compare an apple and orange. Both have pluses and minuses.
Just for your info. I was also considering the D90 and 50D. I read as much as possible and ended up with the 50D. Not because it has 14-bit or more megapixels. It just felt right when I saw and held it in the shop compared to the D90. So go ahead and test them out at the shops. You might think of what justifies the price difference but I think it's not only the features that justify the difference. You will never find rival cameras with the exact same price.
You will have Pro-Canon, Pro-Nikon, Pro-Sony or Pro-whatever supporters. But opinions are opinions. Think about it as objectively as possible. If there was ever a camera brand that is better than the other, there would be only one camera brand in the world. It's all up to your needs,budget, and whatever else that is important to you.