I'm not as sanguine unless Apple increases the screen resolution of the touchscreen on the iPad to 1280x768 or 1280x960 so on-screen fonts can be rendered more cleanly for a better long-term reading experience. I've seen the Barnes & Noble Color Nook and the font quality on the color screen is just phenomenal.
I had eye-strain problems while reading books on my iPad at first, too, even using the Kindle App. I solved the problem by slightly increasing the size of the font.
Now my main complaint is that the iBook application uses up the battery too fast. I can switch the Kindle App text to white on black, but that option does not exist in iBook.
the Latest nook has a screen resolution of 1024×600 and a pixel density of 169 pixels per inch and the iPad has a screen resolution of 1024-by-768-pixel resolution at 132 pixels per inch
Any apparent difference is screen size (6" to 9.7"), which affects dot pitch...but screen resolution is essentially the same.