find the right place for you. Like any other job the work environment and the culture will determine how you fit and how happy you are. I have been talking to so many friends grappling with the same questions that I decided to jot down some ideas that may help others in their struggles or their choices.
In a way or another, universities are corporations for higher-education and that they would do anything in their power to protect their reputation and appeal for students, including throwing their faculty under the bus or swiping problems under the rug. They are companies like many others, with often the difference that their products are teaching and research, and that their administration may not run quite right no matter how fancy they are. Being a great scientist and being a manager are two different things, and while you may be good at both, not everyone is. In addition, once you see how the sausage is made and the money is distributed at the Hunger Games of the Deans, you realize that even the best intentions can be foiled by institutional politics and that academia is most certainly not a "family"...So, how do you find the right place, or survive until you have another chance to find it? Being on the job market as a faculty or postdoc can be quite scary and very "impostor syndrome"-inducing. You are terrified that nobody will want you, and if someone says "yes" you may feel obliged to take the job you can, even if you are not quite sure it's the right one. You might also think it is the right one, and circumstances will change due to the aforementioned Hunger Game results or some other issue.
The most basic criterion to be met is operations: a smooth process in grant submission and management, hiring, ordering and facilities including animal handling if necessary. I haven't heard of a single place that gets a five-star rating in all these things. If you know if this unicorn university, please mention it in the comments...or keep it to yourself so that nobody else can apply. Nobody tells you, but the single greatest source of delays in your scientific progress is having to spend a large portion of your time dealing with admin issues, and these issues hindering the work of your trainees. Plus, the possible development of multiple ulcers. Admins are critical and while there may be no place where they are all efficient, the efficient ones will save your life and help navigate the difficulties of academic administration. Depending on the needs of your research program, you need to find out as much as you can about the different aspects of operations. Ask everyone you meet and look for a pattern of consistency or elusiveness in their answers. Also, figure out if anyone is doing something similar to what you want to do and talk to them, because other people may have no idea of obstacles you may encounter.
Then, as long as you can get work done, there is the scientific environment. Are there people thinking about the same questions you are thinking about? Or tangential questions you would like to explore? Or questions you have never thought about, but sound really cool? Is there scientific and technical support around for you and your trainees? Most new PIs will tell you that their job is very lonely. Often lab heads are hired to fill a specific hole in the departmental expertise. Sometimes they dovetail nicely with other people already in place, sometimes not. The loneliest situation will arise if you are in a place where your expertise is not present and not understood, and where you cannot speak to anyone in depth about your research. Conferences, collaborations, and publications will become the only source of information on advances in the field, and you may be the only expert to provide technical help for your lab, which may slow innovation. There are multiple ways to adapt, such as developing extensive collaborations or changing research direction, but again, asking in advance and knowing what you are getting yourself into always helps.
And then there's culture. I may be hypersensitive, but I find that the academic culture of an institution as a whole defines how happy you'll be as a scientist there and will also define the scientific environment. In a siloed system, the culture of the individual department may be enough. By culture I mean the university's spoken and unspoken value systems. Do they claim to value research? Do they think research increases their prestige, but would rather not pay for it? Do they claim to value diversity? Do they claim to value collaboration and interdisciplinary team science? Do they want to subvert the status quo and hire scientists doing high risk/high reward projects? Do they have a focused mission (cure cancer, solve state-specific problems, etc)? Do they want their names on high impact journals no matter what? Do they aim to be a global or national leader? All these questions are part of different cultures I encountered, and everyone may elicit a specific reaction in you. You may be inspired, or annoyed, but overall how they answer will define whether you would like to be there or not. Even if the answers are great, the next step is to figure out if they are actually embodied by the employees, i.e. the faculty and the administrators. Every single place has a mission and vision crafted by a media office with upper-level dean-types. This doesn't mean the rest of the institution has bought in, and changing institutional culture can take a decade. On a 6-9 year tenure clock, you don't have a decade. Again, look for consistency in answers, but not so much consistency that everyone is giving you a memorized version of the mission statement.
If you found your magic spot, enjoy it. If not, you are most likely wondering how much to compromise and whether the job will provide a launching pad for another job. People in academia move around all the time and you don't owe the university anything, especially if they cannot provide a suitable environment for research. But the grass is not always greener. A university can support your career, be neutral, or be toxic. I am discovering much in this job is about compromise and being pragmatic, so if you are in a neutral environment, you want to think things through. If it's toxic, leaving is a no-brainer. The moment you get money, you have the option to search again and compare and contrast, but it's worth beginning to plot your escape the moment you decide you may want to leave. All information on operations, environment, and culture can be more easily obtained from friends and colleagues at other institutions. As your circle expands you can leverage these contacts for new opportunities. It may take a while for the right position at the right place to open up, and you want to be in the know. The more you go give seminars and meet other scientists at meetings, the clearer it will become what is a good fit...and also what is realistic, since that unicorn university doesn't exist.
Photo credit: By Diliff [CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], from Wikimedia Commons