  I'll be blunt: 1. Poor leadership - they promote people too fast in many instances, and they promote guys who are the "well rounded" vice the really capable (see my entry below). 2. The extraneous BS - there are a thousand and one requirements you have imposed on you that detract from your actual job and duties. Goes back, in part, to the "well rounded" concept, but much of it is just standard military BS that has grown unchecked over the years. Take training, for example; one problem is that quantity is emphasized over quality, and the quantity grows everytime someone up the chain sees what they perceive as a need or deficiency. The result...the average submarine engineering department sailor attends 5-6 hours a week of classroom-style training, this to do a job he spent 2 years learning in schools and another year doing under instruction on the ship to qualify. This is classroom training outside of OJT/drills/practical learning. And the administration of these training programs takes the LPO and Division Officer a significant amount of time each week. This is at sea or in port. Then there is the cleaning - still under extraneous, because (again) of the amount. We once calculated in an average week at sea that most guys do 12-14 hours of cleaning (9-10 watches in a week with a 3 section rotation, doing cleaning for one hour after each watch, plus a 3-4 hour all-hands field day each week...and this doesn't include the time you are supposed to dedicate on-watch to cleaning, which in my experience was directed to be about 1/2 to 3/4 of a 6 hour watch). Throw in drills (1-3 a week in port, three to five drill periods with multiple drills each at sea, more if an inspection is near) and you are looking at about 25-30 hours a week that is spent not doing your primary job...instead, it's training, cleaning, and drilling. Now, those things are necessary...but believe me, the amount of time dedicated to them (which includes, in addition to the numbers above, more time for those who have to prepare the training, or the drills) is out of whack when you consider that, at least in port, there is usually a good 30 hours a week of solid in-rate work to be done (maintenance, testing, repair, ordering parts, scheduling/administrating the maintenance, etc.).
So, on a conservative estimate you spend, in port, 3 hours a week drilling, 5 hours training, and 10 hours cleaning (an hour a day, plus a three hour field day, plus two more in a "responsive" sense, at a minimum) and you have taken up 18 hours of the nominal 40 hour workweek.
This doesn't include watchstanding (which eats up about 4-6 hours of the workday every third day for all your sailors), the time spent in going/coming to/from all this training, and the time getting out/putting away the cleaning gear and reinstalling the stuff you pull up to clean under.
Rough figure is about 20 hours a week doing stuff that isn't addressing your workload. So when does the work get done...when do guys study for advancement (which the ship's training does woefully little to prepare you for, in most cases)...when does the general military stuff (counseling, evals, preparing awards, PT, quarters, mentoring) get done? It doesn't, in a lot of cases. Well, the work does (often rushed, done after hours when guys really want to be home, and thus done shoddily). The rest...well, it gets shoved to the wayside until it is neglected so long that it becomes a crisis.
Oh, on top of all that...to make rate these days you have to be "well rounded", remember (see below). So you have to have your collateral duties, your out-of-field qualifications, all that stuff. When do you do that? Well, many spend significant amounts of their off-duty time doing it (and if you aren't there in the "off" hours you are derided and considered a slacker), many others do it when they are supposed to be working, thus foisting off their work on someone who never gets the opportunity to be "well rounded"...as he's doing the work!
3. Taking care of our sailors isn't important anymore - sure, there is lip service paid and plenty of programs out there, but commands don't really support people who need help. Trust me, I've seen this happen often enough to believe now that this is the norm rather than the exception. 4. The "buddy system" - it's not just for overseas liberty. This, sadly, has been around for as long as we've had a Navy, and I'm sure we aren't unique...but favoritism on the part of (or being disliked by) one's seniors usually makes all the difference in your success...not your ability. Same idea goes if you are in any kind of trouble...if you are connected, you are safe. If not (or if you are not liked) you are screwed. If you rock the boat and try to do the right thing (which often isn't the expedient route the ship/CO wants) you often are the target, and the scapegoat when a head needs to roll. (I've seen this firsthand on several occasions, as well). 5. Organization - or lack thereof.
For all our instructions, memos, policies, procedures, checklists and the like the Navy often is run on a crisis management "chicken with it's head cut off" mentality. The amount of administrivia for nearly everything makes even the simplest of tasks (say ordering and replacing a light bulb) a chore that takes 5 times longer than it would in your house...and kills two or three trees for the paperwork in the process. 6. The "forest for the trees" - meaning we often can't see it. In the Navy, the "big picture" is so often lost we have a term: LOBP ("loss of big picture"...alternately "LOBF" for "loss of big flick").
Sadly, the leadership gets caught up in this the worst...they who are supposed to guide us through the forest get bogged down in climbing every tree. 7. Job satisfaction - this is, of course, a personal issue for most concerned. But I hear/see/personally experience the lack of job satisfaction all to much. Innovation is becoming more and more rare in the era of "if it's not in the book, it can't be done" mentality. There seems to be no real reward, and much of what we do is done out of "it's always been this way" mentality or for no good or discernable reason. How much satisfaction can one get from a job that no one (even the chiefs or senior leadership) knows the reason for, and that has no clear purpose or need to be accomplished. That is, of course, my opinion...others may not agree. But it's many of these things (especially in regards to my last submarine and my observations at my current command) that have driven me to the point of deciding that I'm getting out. The pay and more importantly the nature of the job aren't good enough anymore to put up with shortcomings that keep growing and piling on themselves. 
