If what I am hearing through the rumor mill is accurate -
The first two WP&Y engines coming from NRE are being reworked from new NRE locomotives that had been built as demonstrators for Australia. There are certain changes that had to be made to meet North American practice (particularly the cab controls), changing the gage from 42" to 36" and substituting GE764 traction motors and I'm sure other changes to take into account the different operating environment. Any additional locomotives would be new copies with any modifications found to be necessary or desirable. The term "new" here does include components that have been recycled and rebuilt, in particular the EMD prime mover and traction alternator, and the trucks may be recycled from the demonstrators on the first two.
In contrast, I'm hearing that the units for the D&SNG from MPES are being rebuilt from standard gage commuter locomotives. Obviously new trucks but to what extent the existing frame, carbody and cab will have to be modified is pure speculation.
Based on industry reputation, the NRE units will be the better of the two in quality and design, not to mention it starts from a narrow gage design to start with. This will likely have NRE's own microprocessor control system which they have extensive experience with. MPES likely using a third party system which may have compatibility or support issues.
My opinion - neither will meet the expectations of the customer before reliability, maintainability and costs are even considered. My issue with them is a bad application of the design to meet operating requirements.