Well I can tell you that Prototype is one shore billet that you will work as hard if not harder than you did on the boat/ship. Charleston is a great place to live, as I am sure you know since you were probably a student there for NFAS/NPS. Things are definitely different on the "Staff" side of NPTU than they were as a student.
Prototype is tough, it takes a lot out of you, it will make really hate you job at times. There are countless posts on here about the good, the bad, and the ugly about prototype. You will hear numerous stories from both people here and people at your current command about how it is. Having SURVIVED 3 years on crew in NPTU I can tell you that it will most definitely give you a different perspective the nuclear navy. It can, however, catapult your career in ways that other shore billets can't(depends on a lot of factors, both in and out of your control such as timing for shutdowns, quals, etc).
If you plan on staying in, Go ahead and get that protohell tour over with, get qual'd through EOOW and hope they don't make you go back again. IF you want to get out and want a cake walk till EAOS, better try SIMA or some other billet.