I may as well post my problems with the new MacMini -- I'm on my 2nd (I replaced the first after my external FW drive, which I boot from, kept randomly disconnecting, and even one of the USB ports was faulty enough for my keyboard to occasionally stop communicating. The second new Mini hasn't randomly disconnected yet but I've been VERY careful when inserting or unplugging the FW cable.)
I actually purchased the previous MacMini about a week before the product upgrade, so I have a good perspective on the difference between the old and new. I've booted externally from the same HD on all 3 Minis, a very solid external HDD, and can attest that the FW400 port on the older Mini was MUCH more solid than the new FW800 port.
I know that FW800 has a somewhat less solid plug and port design than FW400 or USB but still, compared to my external HDDs the FW800 port on the new Mini is noticeably looser.
With the previous gen Mini, I had no problem setting my external as the permanent boot drive (in system preferences) and always booted up from it. With both new Minis, I wasn't able to do this -- half the time the external is not recognized and the Mini won't boot up until I turn it off, unplug the external, boot on the internal, plug the external back in, re-set system preferences and restart from the external. As you can imagine this is a tedious way to start up your computer every morning!!! I've tried just leaving the internal as the default boot drive and start up pressing the option key, so as to select the external, but half the time the external does not appear. Even worse, it won't let me boot up from the internal even though it does appear after an option-key-startup and I click on the arrow pointing at it. (this might be an OSX bug, i.e. no starting up with the option key if you only have one drive to choose from.) I suspect this is related to the FW port because it doesn't happen if the same external is plugged into a USB port; however, USB is so much slower and doesn't let me daisy chain a second FW HD for time machine, so just using USB isn't an option.
Apple told me to just exchange the Mini but the same problem has occurred with the second one.
I wonder if this is because of Apple using a cheaper FW chip or module in this Mini, compared to the previous gen. The super long FW thread on the rumors forum includes speculation that Apple has downgraded the FW chips in all the new models except the Pro. I haven't seen this confirmed yet, however.
Another difference I've noticed between the new Minis and the previous gen is that with the new ones, I don't hear the startup chime on my external speakers anymore, only on the internal speaker. Also, there is often a lag between adjusting the volume on the keyboard and the volume reacting, plus there are a lot of speaker hiccups and delays that occur before email alerts or other beeps. (I'm going to see if repair permissions does anything about this.)
Given how crucial the FW port is to me in any case (what with various FW externals and peripherals), I certainly hope that if this is a general problem, they will recall and beef up the FW on this model. Otherwise it seems pointless replacing it every 14 days only to get the same problems. If it's a just a bad batch, it's probably all my local Apple Store has in stock...