I don't see them eliminating the Mini, it's 1/2 the price of the 21.5" iMac for a good reason. Also, the reviews of the new Mini's have been really, really good, and its a product that gives Apple the chance to sell even more $999 Displays, not to mention mice / magicpads and keyboards, and does A LOT of things that the Apple TV can't.
Review of the MacBook were good too when it was released, popular too with vocal proponents, and remember the Mini is supposedly for those who already have their monitors, keyboards, peripherals - not people looking to get new ones. The thunderbolt display while yes may be great for a mini user, why would they go that route that when a 27 inch iMac gets them something much more powerful for $100 (<7%) more? Apple seems more to be marketing the thunderbolt machines as docks for laptops rather than monitors for desktops. And as for switchers, laptops not desktops comprise the majority of first time switchers. So the alternative to a PC solution is being taken up by that.
AppleTV + app store (which it doesn't have ... yet) with integrated iPhone + iPad support through airplay seems to be where Apple is heading with its media center. Again, I'm not saying this will happen next cycle, but two cycles from now? Already from the mini Front Row is gone on the software side and the DVD player is gone from the hardware side ... the main difference between the AppleTV and the mini are now components that given what Apple is emphasizing on how media should work and the role of a media center aren't necessary.
That just leaves its role as home server - easily replaced by a new Mac Pro model.
The Mac Pro becomes the computing generalist acting as part pro-server and computer, part home-server and computer. The Apple TV takes over as a media center and the laptops remain as the main "switch-to" device. The iMacs remain as the all-in-one solution.
EDIT: BTW I am not necessarily advocating for this, but given Apple's past and current moves in product lines this seems to be the direction they are moving.
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