Glad to see a constructive discussion on the Freescale Tower System. When I saw the thread title, I thought it may be best to not touch this with a 10 foot pole, but what the hey I like my Tower System so I thought I would add to the topic. I do work for Freescale so I am some what biased, but I can give you the facts to help clarify your questions. I do think the ad is quite comical, but I guess it worked.
So the Tower System kit is definitely not subsidized. Using the x16 PCI express card edges on modules reduced the cost a lot over traditional berg connectors. If you want to buy 100 for a class go for it. I can put you in touch with the university program folks and maybe they can help get a lab setup.
Glad you like the ColdFire MCU with Ethernet; this is the first of many MCU/MPU modules for the Tower System. In the near future, you will see new plug-in modules that are suitable for other applications. Same goes for the peripherals, I think Ran says it best that there is a need for a "digital I/O expansion" module for rapid prototyping. This is definitely on it's way and will have a protoboard area with access to the Tower System signals that are on the interconnect board aka "Elevator". In the meantime, there are two expansion connectors on the Functional Elevator that give you debug ,probe or wiring access to all the signals.
Other pre-announced peripheral modules is an 802.11b WiFi module, TFT LCD module, and Memory module (CPLD, MRAM, SD, Compact Flash).
On CodeWarrior, I have heard the complaints before just like Coding Badly mentioned. The only thing I can say is give it a 2nd chance. I know there were tons of usability changes done in the past two years to clean up that user experience. If not, IAR and GNU are still options and both all support the debug hardware on the Tower System.
Ok, that's enough from me. If you are looking for a new development system, check out the Tower System; it's only $99 bucks.