Aircraft handling qualities can range from marginal to exceptional and still allow type certification. If after a period in service the aircraft is judged too marginal – may be weather or skill related, etc, then the type certificate / modifications can be considered.
The MD 11 has reduced longitudinal stability compared with conventional aircraft and uses a relatively small horizontal tail. It is (or has been) prone to pilot induced oscillations during the final approach and landing.
IIRC the MD 11 flight control system has been subject to at least one Airworthiness Directive requiring modifications.
Then consider the gear/wing structural design !
http://www.airlinesafety.com/faq/faq9.htm