There are many reasons for me why I prefer Mini ITX over a laptop ...
1. I want to continue using my 24" monitor instead a smaller laptop screen (would never return to 17").
2. I want to be flexible in regards to CPU / memory / HDD ... (upgrading is cheaper than on laptops).
3. I prefer using a full size keyboard over a laptop keyboard (I don't need my PC to be portable).
4. I prefer using an optical mouse instead the touch pad (I know that you can use an external mouse on a laptop).
5. Quadcores are not existing on laptops.
6. Laptops are not always 100% compatible with PC games (and their GPU is usually not strong enough).
7. The inconvenience when something gets broken (with desktops you can exchange the broken part easier & cheaper).
8. Desktops tend to be cheaper than laptops in general with comparable specifications..
9. Laptops get stolen much, much easier ...