Are there any DoD best practices or guidance that contain common down-select criteria or comparative analysis templates? I'm looking for anything that can help me come up with an objective list of criteria (quantitative) that I can add weights to, to aid in the fair selection of one of two prototypes.
You don't specify what type of system that you are prototyping, but that wouldn't really change the answer. In general, you want to choose criteria that:
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1) Reflect the items that are most important to the end user, or, in this case, the system designer;
2) Are likely to be discriminators between competing offerings;
3) Are not too numerous in number.
It doesn't sound like what you are doing is going to be a formal "Source Selection", but, that said, the recently updated Source Selection Procedures (attached) do offer some guidance on selecting evaluation criteria, beginning on page 3.
Specifically, "when developing criteria, consider hybrid approaches, applying objective and subjective criteria as appropriate to evaluate elements of the proposal. Criteria should be tailored to balance objectivity with subjectivity in the evaluation with outcome and to emphasize areas of differentiation".
You may not be doing a formal source selection, but these principles still apply. It is important to first determine what characteristics are most important for the prototypes to exhibit: (Technical Performance? Reliability? Simplicity of Design? Low cost? Low weight? Low power consumption?) and then choose evaluation criteria accordingly.
Don't choose too many criteria, as then it dilutes the "weight" of your chosen areas of emphasis and unnecessarily complicates the evaluation.
Because choosing criteria is very specific to the nature of the items to be down-selected and to the purpose for which they are intended, I am not aware of "templates" that provide a starting point for choosing criteria. The general rule of thumb is, "choose criteria that reflect what is important to the user of the system."