Funding research is, by definition, less cut-and-dry as to what we should pay for; thus having an agenda is not always bad and might even be good. I am using an "agenda" not in a narrow political sense, but including positions like "we should be funding space comms / drone networks / real-time soldier health monitoring / whatever because industry is not building what we think we will need in a few years".
But being somewhat exposed to the waste of DoD procurement I am personally vehemently against inserting such ideology into procurement decisions. Those should be money-based. Get what you need at the least cost to the taxpayer. If you do not know what you need, think harder or invite experts or do a study (and publish it so people writing it know they are associated with those decisions) before paying billions for questionable junk. My 2c.