Pay. Pay sucks. When you come to MITRE, you will receive a fair offer that will be market competitive. However, your yearly increases end up putting you well below market in 3-4 years. So you you ask -- "why do people stay rather than leave?" because make no doubt about it, over half the company has been there for 15+ years. This answer is two-fold: 1) you are a mediocre engineer and frankly couldn't get a job elsewhere 2) you are an absolute rockstar, best in the world, and on a really kickass project that you absolutely love. Unfortunately, MITRE is on a trend towards more #1 and less #2. Frankly speaking, they're a not for profit and shouldn't be expected to be competitive in pay since they make up for it in work life balance, etc. But there is a trend where the old talented engineers are retiring, the young talented engineers are moving to startups, and you end up with under-performers who would be fired at any other company.
Another reviewer put it best -- "MITRE is a great place to work as little or as much as you want". MITRE is that now ex-girlfriend that you wish you had ended things with several years ago.
The company is convinced it's not a software shop but in several of the departments, that's just not true. And common software development practices of testing, continuous integration, using source control, commenting code, etc. are just not followed.
The promotion process isn't great. You basically put in your time rather than being promoted based on performance. For example, if you have a masters and come in as a level 2 (e.g., software engineer), you'll hit level 3 (e.g., sr. software engineer) in 18-24 months regardless of how good you are. Going from level 3 to level 4 will usually take 5-10 years and again depends more on your networking ability or department rather than skills.
So if you're a rockstar engineer who wants to do good things in the world, get a job at MITRE (let me or someone else validate the department / project you choose!) However, you'll do yourself a disservice in staying there longer than 3 years which sucks because, as a rockstar, you'll be on a really fun project.
Alternatively, if you're not the best engineer (or prioritizes life over the job) who wants to pull a decent paycheck for the rest of your life, this is the company for you.