Best way to transfer to another Mac

Recently, I had to restore my Mac from a Time Machine backup due to some issues I was experiencing. Although the backup restored my applications, all of my preferences, settings, and ssh keys were reset, leading to a significant amount of work after the backup. I am looking to buy a new Mac soon, and I want the transition to be much smoother. Will using a Thunderbolt cable to transfer provide a more complete restoration than Time Machine? If not, are there other ways to more completely replicate my old computer to a new one? I don't want to reconfigure all my settings after I get a new computer.

Some context:
I was using the OS X Yosemite beta when I decided to restore back to Mavericks. However, the instructions Apple provided for doing so were not working, so I had to take a long alternative route. I used Internet Recovery to restore my system to OS X Lion (10.7), updated to Mavericks through the App Store, then used Migration Assistant to restore my computer from a Time Machine backup. In the process, I had to create a new user account (after Lion was installed). Maybe this is what caused the issue, but shouldn't Time Machine still have restored everything properly?

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