Interesting that after seeing this thread I had a read of the reports for the Merpati MA60 accidents. These along with the witness/media reports from the other accidents at Zest and Myanma do not indicate a problem with the aircraft at all. Both Merpati accidents were purely pilot error.
PK-MZK Flight 8968 (7/05/2011) was a visual approach into IMC (vis less than 2000m) , no briefing at all prior to approach, no navigation facilities or instrument approaches available, PIC called for flap settings that did not exist on the aircraft and during the missed approach called for flap retract below retract speed, never set climb attitude, in fact set 1-2 degrees nose down at 300AGL and entered a 38 degree angle of bank turn.
Flight 6517 (10/06/2013) The flight where the aircraft landed hard and lost its wings/engines. In the preliminary report Merpati was found to have changed the approach checklist to disable/turn off the automatic flight idle stop mechanism against the manufacturers checklist. The aircraft performed a non-stable high approach and the left engine was found to have been in beta from around 200agl to impact.
The two Zest over-runs appear to be more a matter of not enough runway for the aircraft combined with poor conditions and very bad pilot technique. The Myanma accidents were similar and the same airline had managed to lose a few Fokkers in years past as well.
I don't know much about the aircraft in detail, however the accidents do not seem to reflect a problem with the aircraft rather more a large problem with training.