When Flying out of Morelia Airport it is best to just have carry on luggage. At check in every bag being checked at the ticket counter is open and manually inspected. Carry on luggage gets you to the head of the line. It will can be up to a 4 hour wait at the checkin counter
Even though flying through Houston (IAH) can be a bit of a scheduling issue, using Continentai Express for their jet commuter non-stop service (presently two a day) into and out of Morelia (MLM), makes a lot more sense than facing the insanity of the Mexico City Airport. The flight from Houston takes about two hours and it is easy to burn up that much time and more just trying to claim bags, clear customs, and navigate the congested traffic conditions of the Mexico City Airport.
When flying out of Los Angeles (LAX), Mexicana is the only airline that flies to Morelia. Anyone else will partner with them. It is in your best interest to try and upgrade to first class when you get to the counter. The cost is only around $100.