It is the government, so when it comes to actually getting something done people tend to act on their own time frames. Also, the number of tracking numbers for a single item is mind blowing, I once had a two page boilerplate letter to be signed by the regional administrator and it had to get 4 tracking numbers and took 2 weeks to jump through all the hoops. And god forbid you need something done on a Monday or Friday, Mondays are basically catch-up days and Fridays have a skeleton crew. Not to mention holidays, if there's a holiday that week you can expect the more senior employees to take the week off (they accrue time off at the rate of 8 hours every two weeks, aka every pay period they get another day off). Add that to the crazy flexibility of the work schedules there's people that only come into the office 3 days every two weeks, and the days they work from home it's like they're basically off.
In addition the technology has only recently caught up to modern standards, and since most of the people working there are over 50 it's tough to get people to try the newer forms of Microsoft Office without walking them through everything (some old-timers still use wordperfect and lotus123 for official business). Also, the number of passwords and programs that have to be logged into on a regular basis are overwhelming. There's a separate program/password, each, for entering your time, viewing your paycheck, managing your retirement, managing your health insurance, managing your pre-2013 email, (this is important due to FOIAs/federal records management) managing your post-2013 email, elearning, and on top of that your computer password and 8 digit login id number, all of which must be different and have to be changed on different time schedules (some every 90 days, other every 100, 150, or 180 days). Another con is definitely HQ, if anything ever has to go through them it takes an ungodly amount of time and pestering.
Again on the technology front, most companies are taking advantage of electronic signatures and other electronic time saving ideas, but the government is slow to catch on and in some cases is not allowed to catch up. For example, for records management if emails are records they must be printed out, scanned, and made pdf searchable (one of the reasons people don't do records management or prefer not to leave a paper trail - it just takes an ungodly amount of time). Another example is electronic signatures, from what I've heard the government is completely against allowing management to electronically sign documents.
The last con I have is that they are now making most career ladder positions stop at a GS-12 instead of a GS-13. This is the way things used to be in the 1980s, but now almost everyone that's been there long enough has a 13. So now when they hire new people they'll never get that extra pay and retirement contribution as their colleague in an identical position gets. Also that 13 employee won't ever be asked to do any more than the 12, the 13 will never get knocked down to a 12, and if the 12 gets promoted to a management position they will be on the same grade level as the people they supervise, but they might get paid less due to step levels.