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The Mac Mini may very well have served it's purpose - especially once the move to the Intel platform happened.

One of the stated goals was to allow Windows and Linux users to "try" the Mac OS in a more cost-effective form without having to go "all-in" with an iMac or Mac Pro. I myself hemmed and hawed for some time about adding a Mini and a KVM to my existing PC system to experiment with OS X before I decided to replace my 17" HP laptop with a 13" MacBook when the latter was first released. I was the only person in my circle of friends who did not use a Mac as their daily machine and I wanted something smaller for travel (as well as figuring it would be more helpful to have a Mac when I visited them), so the MacBook made sense.

We're now into the third year of the "Intel era" at Apple and two years into the Mac Mini with the Intel CPU and Boot Camp. While I fully expect there is still a market for the current Mac Mini amongst those who wish to "experiment", over time the market for such a machine should continue to diminish as folks either stay with Windows/Linux or they commit to OS X fully and buy an iMac, a MacBook (Pro), or Mac Pro.

IDC and Gartner both note that computer sales (especially notebook sales) continue to strengthen worldwide and Apple's 37% increase in desktop sales and 61% increase in notebook sales last quarter reflect this growth. So perhaps it is becoming time for Apple to branch out and add new models.
 
I'm not saying this is a good thing, but we have seen that Apple is not happy with the idea that people may be combining different parts..

What do you base that statement on? The Mini is marketed as "bring your own keyboard, display and mouse." The Mac Pros are designed to work with a wide range of third-party hardware.
 
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