ONLY use TM restore when you're restoring to the same computer. For example, if your HDD crashed and you installed a new HDD, you can just restore (basically it just copies the original "image"), all your settings and files are restored.
If you're upgrading to a new machine (or if there's the slightest difference in hardware between the two machines) you should use the migration assistant to migrate files from your TM backup. When you start up your new Mac for the first time, you'd be asked if you want to transfer files from another mac, you can either plug in the old mac Mac with FW, or simply plug in the external drive with TM backup (USB is fine too), and most, if not all files and settings will be transferred seamlessly.