Compensation. Period. If you're not an engineer, you will definitely come in at a below-market salary. The company changed it's promotion structure to make it harder for young employees to get their money. We've already begun losing young promising talent, and this will only continue to happen.
Dead Weight. There's a lot of it. And overpaid, too. It can be found in all functions (Program Management, Contracts, Subcontracts, Finance, Billings, etc.). This has a life-sucking effect on morale, which has continued to steadily drop.
Also, even though we are "salaried" employees, the company expects us to work a certain amount of uncompensated overtime (which is tracked) every year. This is factored into promotions, raises, etc. The result is employees having to play a game just to advance their careers. Management doesn't care that some people just take a lot longer to do the same job as others.