Not to say whether to keep or get rid of prototype, but the electricians we get never seem to understand the electric plant. We have to teach them how to operate the EPCP. I'm pretty sure AC paralleling and the electric plant layout is virtually the same on S5W, S8G, and S6G, yet you have to fight to extract the paralleling requirements from them. It took me a while once on board to figure out the EPCP, but I'm an ET, so I didn't learn it in prototype. Still, its not that complicated. And I also thought part of the point of prototype was to teach students how to use the phone circuits, yet we consistently have to train all the new SEOs how to use the damn things.
So as far as mechanics go I say that we can send them out to the fleet immediately after NPS. EM and ETs I feel should have about a month or so of IDE type hands on experience just for the sake of operating switches. Very minimal overhead for that... EOOWS should also go to the IDE type atmosphere and get some hands on training there. I only say this because I personally saw an EOOW that was super stellar in NPS, but couldn't supervise the plant to save his life or anyone else's.
I thought about this, then I read your post, curse you for beating me to it.

To add a little to it: Mechanics need exposure to a plant before they go to the fleet. But I don't think it needs to be operational exposure. Rather, set up the program so that during NFAS and NPS students can go down to the MTS and be shown what they will be working on in context, perhaps even get in there and operate, under close supervision, SSTGs, HPDs, feed pumps, etc. I remember the visual aids we had in power school, it was a room full of equipment that wasn't connected to anything, was just sitting there, leaving us to imagine (wrongly) how it fit into the plant physically. The fusion of the two curricula would necessarily lengthen NFAS and NPS, but eliminate the need for NPTU. For EMs and ETs, a lot more hands on work could be built into the NPS side, so that after learning about reactor theory or electric plant ops they could go and conduct startups and shutdowns on an IDE, shift the electric plant, learn about casualties, then see them run on a simulator, learn the theory behind the CPs. I remember a simulator at NPS for the EPCP, but a full IDE would be more useful, also we didn't get more than about an hour to look at the EPCP simulator, and it was shared among 25 of us.
Also, I thought the MTSs were just training platforms. Are they still used to test new equipment or is that only done up in Ballston Spa? And, just a comment, but there is no prototype for the Virginia class. SSN 774 is the prototype. Proves the necessity from that end. Though they could have used a bit more testing on some of the equipment, as it seems prone to catching fire, but its nothing prototype worthy.