Moving files from a Time Machine backup manually vs restoring from a Time Machine backup

I have read several articles saying that contemporary Macs and OSs are built such that they clean themselves up - defragmentation, general sweeping, etc. I was told by the Genius, however, that there are many little files that are left lying around after installs, uninstalls, file making, and file deletion that will gum up the works. He recommended that I set up my computer as though it's brand new and manually transfer files over from my Time Machine backup folder on my ExtHD.
Because I couldn't find a discussion of this specific topic online, I thought I'd bring it to the community myself. Is there an advantage to setting up the computer from scratch and manually moving the files (provided I use Migration Assistant for applications)?
For background:  My Mac was running slowly, and after doing some research and talking to a "Genius", I thought it would be wise to reformat my HD and restore my system. Aside from sluggish performance, I was experiencing strange symptoms - like free disk space remaining the same even after deleting huge files, permissions errors, etc. I tried doing a permissions repair (a process I'd been told to do before when experiencing issues, even though I never knew what that really did), and read that I should verify my disk as well. Disk Utility told me that I had to reboot from the repair disk to perform the necessary repairs. The repair disk Disk Utility told me that my disk had some major issues and needed to be reformatted and restored.
HOURS LATER: I am back up and running now and Disk Utility is showing the appropriate amount of free disk space.

Let's start with some basics.
Check under the Apple in the Menu bar About this Mac > More Info
How much Memory do you have installed?
What size is our hard drive and how much free space?
You'll find the term Genius does not necessarily mean they are expert. Even on this forum, you'll find varying difference of opinions and levels of expertise.
I have read several articles saying that contemporary Macs and OSs are built such that they clean themselves up - defragmentation, general sweeping, etc.
This is true. Apps like MacKeeper, CleanMyMac, TuneUpMyMac, Washing Machine or anything like these apps might appear to be helpful, can do too more harm than good. As a result of the 'cleanup' it can leave your Mac non-functional Mac. The forums are full of users with computers that no longer work correctly after running these so call 'cleaners'
https://discussions.apple.com/docs/DOC-4171
Your Mac runs maintenance in the background for you > Mac OS X: About background maintenance tasks
http://support.apple.com/kb/HT2319
I was told by the Genius, however, that there are many little files that are left lying around after installs, uninstalls, file making, and file deletion that will gum up the works.
I'm going to disagree here. Get rid of the installer from downloads after installing. After removing an app, most of the little files do no harm and take up very little space. However some applications mostly crapware/cleaners will leave files that continue to run silently in the background takeing up resources.
Don't install stuff you don't really need. There is no magic bullet to clean up your messes.

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