Besides the great coworkers and environment, flexible hours, and lack of micro-management, which all sound great, the issues such as salary and raises, amount of work you put in, etc. eventually drains your morale.
Salary and raises were sub-par and unproportioned to the amount of work and responsibilities taken on. You could receive a vast amount of praises throughout the year about how hard you're working, or what a great job you were doing, or how busy you were, just to receive a 3% raise at the annual review. The praises feel like fluff blown your way to keep your morale up and going until you get hit with the reality that you are undervalued and probably being paid less than your friends at other companies.
Yes, the banked time helps but that's time that you have to put in yourself for working overtime and was not paid at a different hourly rate (i.e. not time-and-a-half = work more than 40 hours a week at your standard hourly rate). Also, there wasn't a non-billable task to record time spent doing non-project-specific tasks like overhead work. So you either had to bill the time to a project, or spend unpaid overtime to do daily/weekly administrative tasks.
No raises or incentives given when you become licensed or at your annual review after you've become licensed during the year prior to your review. Cost of books and classes for PE are not reimbursable.
Sometimes disorganized where lack of communication led to issues in the project and/or being overworked (see below about prediction of workload).
The predictions of workload were nearly never accurate. Not surprising as it's difficult to do given that some jobs go on hold randomly and others come back to life suddenly. Also, the workload predictions resulted in too much chaos by switching projects between engineers and created more work to pick up on someone else's assignments and train-of-thought.
Although there were lots of great people and mostly tried to be inclusive, it was common to feel that the environment was "clique-y" where new employees could really feel isolated if they were not outgoing and/or overly social.
The downside to the lack of micro-management for a new hire was coming from another firm where I was taught certain ways to do things and being corrected later in the projects of how I should have done it to align with the standards of the group/Principal. Due to lack of micro-management early on ultimately resulted in spending hours redesigning things. Although it was good experience, it was very strenuous and draining.
Sometimes thrown into meetings alone when originally scheduled to go with my Principal - great experience and opportunity to take initiative and grow, but also very difficult and traumatizing when it was last minute and the importance and productivity of the meeting surrounded his vast knowledge. Definitely felt like I was just wasting everyone's time when my only responses were "I'll get back to you after I look into it".
