A negative - At one time, you could replace Moodle files just by pasting the new Moodle over the the old one. A real NO NO, though, as sometimes new versions did not necessarily use all the the same files/filenames, and you would get unexpected problems from those left over files lurking in there with the new ones. Newer Moodle versions check for this and won't allow it.
Another negative - The replace method now basically means you have to have an empty folder to put you new Moodle files in. No biggy, if you don't have any add-ons. If you do use add-ons, you will have to get them back in there to get a clean finish to your upgrade. You see people asking for help in the forums with this problem on a regular basis.
Two positives - Using GIT can eliminate both negatives. Just using GIT will automatically eliminate the first negative. The second negative can be set to be automatically eliminated by adding the folders of add-ons to the exclude file that will be located in ...yourmoodle/.git/info/exclude once you switch to using GIT. This is REALLY handy in my Moodle 2.6 dev site where I try out LOTS of addons (currently 58).