FruityLlama , I think their impatience with your mood in the morning might be because they take it too personally? Moon-Mercury in close aspect like that can be touchy, and it makes people extra sensitive to words. So, even though it seems like a short spell of irritability to somebody else, to them it'll feel horrible.
As for your other question - I don't think squares show intolerance in and of themselves (if anything, Saturn might). Squares make the relationship between those planets very "loud". They're like a very argumentative couple. Mercury is fairly neutral, so the planet that aspects it influences the style of thinking and style of speaking. Mercury square a planet may go overboard in communicating or thinking in that style and the challenge is to balance it out with the qualities of Mercury itself.
For instance:
Mercury-Moon:
Emotive, sensitive. But perhaps too emotive and too sensitive.
Balance needed: Mercury rationality and objectivity.
Mercury-Venus:
Charming, loving, affectionate. Danger of glossing over unpleasant thoughts or conversations.
Balance needed: Mercury calm and diplomacy.
Mercury-Mars:
Sharp, quick-witted. Might get sucked into too many arguments.
Balance needed: Mercury neutrality & logic over the "need to win."
Mercury-Jupiter:
Philosophical, funny, great story teller. Sometimes philosophizing turns to pontificating and identifying too much with one's beliefs.
Balance needed: Mercury's dexterity with details and ability to listen.
Mercury-Saturn:
Sensible, thorough, no-nonsense. The world needs a bit of nonsense, loosen up! (I should know, I have the square).
Balance needed: Mercury openness and flexibility (it won't kill you to change your plans).
Mercury-Uranus:
Innovative, free thinker, genius. In your hurry to get your ideas into the world, you might put the cart before the horse.
Balance needed: Mercury's ability to slow down and work out the kinks.
Mercury-Neptune:
Creative, poetic, visual thinker. Well, having dreams is great as long as someone can transcribe them for you.
Balance needed: Mercury's ability to observe, retain, and translate Neptune's vision.
Mercury-Pluto:
Detective, researcher, formidable opponent. Whoever said "sticks and stones..." never met a Mercury-Pluto person (or Scorpio mercury for that matter).
Balance needed: Mercury's lightness and refusal to be bogged down.