I have recently gone through the pipeline and am now on medical hold on a ship.
1) A school and Power school are pretty much cut and dry. You are constantly supervised, your hours are VERY straightforward, and you work a 5 day work week with some study time on the weekends. the amount of time you spend at work depend 100% on your ability to pay attention, take notes, ask questions, and apply the knowledge you have learned.
2) Prototype is VERY different. You get subjected to 12 hour days in a schedule like this - 7 days of 7 am - 7 pm, "2" days off (you will understand), 7 days of 11 am - 11 pm, "1" day off", 7 days of 7 pm - 7 am, "3" days off, 4 days of 7am - "7"pm, 4 days off. repeat this for 4 months. The problem with Prototype is the lack of supervision. You pretty much make your own noose at prototype. If you work hard, keep your nose clean, and bust your butt, you will notice your time is a lot easier then others. However, since you dont have people over your butt 24/7, its rather easy to slip into a vicious cycle of slacking off. Dont be one of those guys.
3) once you report to the ship, the hours stabilize in port/shipyard, however you are more pressured to qualify and support your watchbill. However, theres still a lack of supervision, so you get the same "make or break" thing at prototype. HOWEVER the key difference here is that you live and work with these people for the next 4-5 years!
Basically with prototype and shipyard/port (I have not gone to sea, so I wont skepticize what happens), the old adage "Dont crap where you eat" applies. Oh yeah, and enjoy 4 section duty when the rest of the ship has 8 section

Prepare to work harder then you have ever had in your life.
As for the bad things, the navy is what you make of it. Each person has their own good and bad things that are unique to them.
Good Luck!