Do not perform a manual transfer - trust me. (Unless it's 2 folders on your desktop.)
Migration Assistant is great because it transfers only your personal data and Applications, not your operating system. This means your personal data transferred is moved to a fresh, unused operating system. You can control what comes over in 4 categories:
Category 1: User Account
Sub-category: Which folders within that user folder (i.e; Pictures, Movies, etc.).
Category 2: Applications (all or none - you cannot choose which ones)
Category 3: Files and Folders (same as Applications - you do not choose which ones)
Category 4: Preferences (I think..)
Also, you'll want to run M.A. right away - if you create a new user account on your new Mac, and then use M.A. later, it does not move your old data into the account you've already created, but will create another
user account. (Seriously, don't go down this road. If you're using M.A., use it right away
when the new machine boots up, and prior to even being given the option to create a user account from scratch.)
If you have a TM backup, you can restore the data from that backup to the new Mac, bypassing M.A. entirely.
Whether you restore from a TM backup, or use M.A., your new Mac will look identical
to your old one.