Best Way to Move from old iMac to New?

My super sweet new 27" iMac is due to arrive next Thursday and will be replacing my mid-2007 iMac. Each OS release has been installed on the 2007 iMac as an upgrade and hasn't been cleanly installed since it was new.
Though I use TimeMachine, I was under the impression that using TM as the migration tool would bring along all of the system files and I wanted to start as clean as possible. So, I had originally set my mind to using the Migration Assistant when the new iMac arrives, which would allow me to have a "clean" system along with all of my apps/files/etc.
BUT... today I was setting up a new iMac for someone, migrating from another iMac that was about 1 year old. Because it had never been upgraded, I decided to the TimeMachine drive. So when initially setting up the iMac, I was prompted for the migration options: from another computer, from another disk, etc. I chose "from another disk," which then presented me with the options expected through migration assistant ( applications, users, etc ). After continuing, I am confident that none of the system files came over from the TM backup.
So... I am not thinking that using my TM backup and the "migrate from another disk" option may be the fastest migration method and still preserve the clean integrity of the new system.
Does anyone know for sure?
tia,
Bill

A few more things about what you can expect with Migration or Setup Assistant --
* The "time remaining" calculation is not very accurate. It might indicate 16 hours to go when there is really less than an hour (or vice versa).
* Wireless migrations take a long time (many hours sometimes).
* The migration is smart enough to not bring over an older version of, say, iPhoto, when your new Mac came with a newer version than you had before.
* After the migration, SOMETIMES (not always) you may be prompted to enter a user code or key for software from Microsoft, Adobe, etc. so have those ready.
* You will probably have to reinstall your local printers and their latest drivers to work on the new computer.
* Setup Assistant running on first boot up before any users have been created on the new computer is the best way. Then your new computer (with the exceptions noted above) will look basically just like your old one after the migration. If you use Migration Assistant instead of Setup Assistant, don't create a user with the same name as you had on the old computer, instead create a generic user called "Admin" or something like that, and then the migration will move your entire old account and user name over to the new computer (if you already created that same user name on the new Mac, it will have to give your migrated user a different name, which bothers some folks).

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