How come moving files on my phone when it's connected to my computer actually does a copy instead? So, I copied a file from my desktop to the phone's microSD card. Then I realized that I'd like the file to be in a subdirectory on the card, so I initiated a move. Shouldn't take long at all, as it's just a file system entry update and not an full copy, right? Wrong! I had to wait the same amount of time as the initial copy! What's the reason for this? Is it some limitation of MTP?
I would really need more info to give you a precise answer, but I think I know what you are speaking of. When you move a file through MTP with your mouse, on your computer, your computer is not just moving the file... it is a totally different type of filesystem, and therefore has to basically read the file and write the file in new location. It is not the same as if you were in adb or terminal issuing: 


  mv FILE NEWFOLDER/FILE


...or a root explorer long pressing to move, which issues the same as above.