Can't say I'm surprised by the report. I've always felt the whole argument about what-it-takes-to-bring-a-gallon-of-gas-to-the-battlefield-somehow-being-obviated-by-alternative-fuels promised too much, in part because you still needed to bring whatever was necessary for the on-the-spot brewing of fuel, plus you now just have a different sort of depot to guard. But yeah, you will cut down on the sheer volume to be moved over the long haul. On the electricity generation, I could get that. Go solar and you're not humping the additional fuel-case closed. I just didn't see why the military should lead any efforts there. Better to simply take what the private sector had and adapt. I've also sort of understood the aircraft fuel argument, although there you're often talking sites not that hard to supply (e.g., a big base may be within flying range of the theater but not actually in it).
Anyway, the whole argument just seemed like it was being driven a bit too much by the isolation-of-Afghanistan notion and all of a sudden here we're talking about the Pentagon's budget becoming this leading force for energy innovation in the economy (the old Internet argument, noted here).
There has been that tendency in the post-Cold War era: you can't get your pet gov-sponsored R&D bit anywhere in the Feb budget, so you declare it a national security issue and stuff it in there. And you had to feel that some of that was going on.
In the NYT piece, the Navy does complain that their programs weren't adequately surveyed, and you have to pause there, because you think of past Navy efforts with small nuclear power plants. Plus, that's a need that's global and rather unchanging, so if a cheaper, better alternative is to be had, then definitely the Navy should go for it.
I don't think the report will be enough for all these programs to be discontinued, but it probably will stop some additional piling on of new ones, which is probably good.
The military is such a microcosm of so many other problems in our economy/society, with spiraling health costs, a hard-to-sustain pension plan, energy costs too much and so on, and with the military's huge budget and reputation for innovation, there's the temptation to think answers can always be had from within. The problem is, of course, that the more non-combat stuff that gets stuffed into the budget, the less it's about the actual fighting and operations and the more it becomes this giant venture capital pool.
So it's good to see some skepticism from the think tanks.