As someone who was able to take advantage of one of those programs, I agree. It really doesn't make sense to me that they would send post DIVOs to get a graduate education and never assign them to a billet to use that education unless their warfare community decides that it doesn't want them several years from graduation. However, since JOs attending these programs still have their primary designator, they have to ultimately continue to support that community. In my case, the Navy is paying me to be an 1120, and not to be an analyst for an N-code in the Pentagon.
Thus the solution to poor ROI on grad education would be not sending O-3's to NPS/MIT/wherever, which is opposite of the suggested expanding of such programs to enhance retention. These programs would be reserved for O-4+ who laterally transferred out of their warfare communities, similar to what the Army does. Even still, there are a limited number of jobs that could support such a program.
As it stands right now, the Navy seems to send JOs to grad ed because that's when it would least impact most officers' careers. If they end up washing out from their primary community at some point, the Navy can still find a use for them with a subspecialty code. It's not the most optimal use of taxpayer dollars, but the more fiscally responsible alternative would make it worse for JOs seeking grad ed opportunities, not better.
For those who want to use foreign language skills or use a master's in engineering to work on the design of the next fighter, there are government organizations or government contracted companies that do these things...just not the Navy.
Or...the Navy manpower system just isn't too good about identifying desirable skills for billets, especially when the demand signal is only temporary.
I had a job that was billeted for an EOD O-4 with a Master's in Computer Science. I obviously am not EOD, and the extent of my Comp Sci knowledge then was 2 classes in undergrad.
What would have been ideal for the job would've been a SWO JO (or Surface EDO) with a Strike or FCO background, with grad ed in missile guidance, aero engineering, or radar/EW. This isn't just a wish list, the program actually worked issues related to each while I was there, and more trained manpower would have been useful.
But that's how it was before I got there, and how it still is years after I left.
Unless you're suggesting all the URL staff jobs that could benefit from graduate education should just go away, or be second tier jobs (and for the SWO community at least, those Pentagon N-code jobs are actually competitive billets), the Navy still "needs" some officers with AQDs. Just because it currently does a shitty job of matching skillset with records with billet doesn't mean you should throw out the skillsets.
Also, Marine JOs do go to grad school (NPS). They screen to identify who they think will succeed in the programs, tell them to go, and send them to payback tours at MARCORSYSCOM or the Pentagon. And the guys I met did not switch out of their MOS's, they were aviators, infantry, commos, etc.