We've done Saturdays in the past and we've been fine. Sometimes we've been pleasantly surprised with the ease of touring on that day and were flexible enough in our schedule to make a full day of it. Other times, it gets jammed with people to the extent where it's no longer any fun and we leave.
EMH contributing to crowds is a given. If you only have two days to do MK and MGM, I think its a given that MK would be the one to do on Saturday. If you get to MK at park opening, you'll get a lot of touring done the first hour or two of the day. With young children, we usually focus our early park time on getting Fantasyland attractions done.
Hope this helps! Good luck with whichever you end up doing!