As promised in “Deepwater is Not the Problem,” comparative performance data for surface and seafloor BOPs follow. Every study and informal review that I have seen has indicated that subsea BOPs are more reliable than surface BOPs. These data are not surprising. Because of the time and cost involved in pulling and repairing subsea stacks, preventive maintenance programs tend to be more comprehensive.
The studies cited below were completed 10+ years ago, but to the best of my knowledge the conclusions are still valid. If there are any more recent studies, BOE would like to hear about them.
Recent data indicate surface BOP reliability is only one-tenth that of subsea BOP equipment.
Subsea BOPs have smaller failure rate than surface BOPs.
SINTEF study: This study is limited to seafloor stacks, and shows there is no difference between failure rates for deepwater and ultra-deepwater wells.
(For wells in >400 m WD) It seems that there is no correlation at all between the failure rate and the downtime related to the water depth.
Sintef Subsea BOP Reliability Study (click to enlarge)
Bud's Offshore Energy (BOE) 
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