First let me say that if you're having focus problems that can't be resolved with some of the suggestions that have been provided, consider returning or exchanging the camera. There have been some bad XSi copies reported and you may have one of them. Fortunately, like many others, I've had no problems with mine.
Please don't think I sound crazy but I was under the impression that the pictures would be better quality with the 12.2 and I would be able to enlarge more.
A 12 mp file allows you to crop more without a significant loss of image quality. And, yes, you should be able to make very large prints with more megapixels. However, a 12mp image doesn't look overly sharp when looked at 100% on a computer screen. A 12 mp image may indeed look less sharp than a 6 mp image. However, when reduced in size and printed, you should see little, if any, difference.
I'm assuming you do basic editing and after reducing an image in size (even at a proportion for a large print), slight sharpening should bring out detail.
I printed the pictures on 4x6 and could quickly tell which camera was which.
Hmmmm, if this is the case, then I suspect the problem is with the XSi.
Another thought, DSLRs let you adjust sharpening settings. Have you tried increasing the amount of in camera sharpening?