First, by running only repository software, at least in Debian, there is a lot less chance something will crash or cause conflicts with other software (that's why they call it stable). Second, when you run only software from the repositories, you are trusting only ONE source. Whenever you add a PPA you are trusting more and more sources, opening door for attacks (let's say an attacker can't get into Trisquel or Debian repositories, but they get to invade a PPA, and add an update with anti-features in it). I read that maybe when next stable comes out, Debian will also ship with Mate, but until then we are left with PPA.

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