• Facilitating mechanical ventilation (MV) typically requires an artificial airway e.g. endotracheal tube, tracheostomy. Inserting these is not without risk, both short- and long-term. A first hurdle.
• The respiratory tree from nose - to - bronchi is crucial immune defence, helps humidify and warm inspired air and helps clear mucous from your lungs. With MV the presence of said artificial airways bypasses these beneficial mechanisms.
• MV is essentially backwards. When you inspire naturally your diaphragm contracts to (in short) create negative pressure in your chest, drawing air into your lungs. When you're done inspiring the elastic recoil of your chest etc. pushes air out. This is called 'negative pressure' ventilation. MV is 'positive pressure' ventilation - it blows the lungs up like a balloon with each mechanical inspiration, then they deflate elastically during expiration. This creates issues whereby the alveoli can be subjected to an unnaturally high pressure (barotrauma) and sometimes also volumes of air (volutrauma). Neither are good and have a host of possible short-term (pneumothorax, ALI) and long-term (CLI) sequelae.
• Ventilator-associated pneumonia. Normally you swallow or spit out your saliva and other upper respiratory tract secretions. When you've an artificial airway in place, these secretions accumulate at the point of the airway's cuff (a small balloon that helps stop it moving). These accumulated secretions contains normally harmless oral bacteria, but over time they'll develop a biofilm, bypass the cuff and enter the lungs causing a pneumonia.

There are other reasons, though I have to go to work now!

Source: Anaesthetist/intensivist