Clean Install of Mountain Lion

Hey,

I currently have a MacBook Pro with Retina display, had it since it was released and it came with Lion and I've since upgraded to Mountain Lion when it became available. I've been using Macs for 12 years now and always use the Migration Assistant at startup to automatically transfer over all the data from my previous Mac as I'm sure other people do.

Since owning my rMBP there are a few minor things that aren't quite right and I don't know if it's just a problem with the OS that will be fixed over time or if it's old data that Iv'e copied over that may be having an affect on the system. Amongst a few of the issues I'm having is that if I choose my own folder full or wallpapers and set one as a background when I restart the folder is missing from the list and the system reverts back to the last used pre-installed wallpaper. Another isse is that whenever I open a Finder window or dialog box if I want to Open or Save a file it will switch the layout, so instead of being in icon view it may auto swithc to list view and vice versa and it doesn't remember where it was last opened at if I need to use the open option a few times and have to navigate all the way through again. Lastly, if I arrange contents of a Finder window by Name as an example nothing happens, I have to sort by some other criteria which then works and I then have to go back and sort by my original option.

That's just a shortlist of many minor issues I have and didn't know if it was just bugs or if a fresh install would help resolve some of these issues.

I back up via Time Machine so would want to transfer all my data back onto my Mac after the new install but how can I make sure all my files, apps, content and other data is transferred over without bringing any crap system files that I probably don't need or might be what's causing any issues?